Soybean variety XB31E11

ABSTRACT

A novel soybean variety, designated XB31E11 is provided. Also provided are the seeds of soybean variety XB31E11, cells from soybean variety XB31E11, plants of soybean XB31E11, and plant parts of soybean variety XB31E11. Methods provided include producing a soybean plant by crossing soybean variety XB31E11 with another soybean plant, methods for introgressing a transgenic trait, a mutant trait, and/or a native trait into soybean variety XB31E11, methods for producing other soybean varieties or plant parts derived from soybean variety XB31E11, and methods of characterizing soybean variety XB31E11. Soybean seed, cells, plants, germplasm, breeding lines, varieties, and plant parts produced by these methods and/or derived from soybean variety XB31E11 are further provided.

FIELD OF INVENTION

This invention relates generally to the field of soybean breeding,specifically relating to a soybean variety designated XB31E11.

BACKGROUND

The present invention relates to a new and distinctive soybean varietydesignated XB31E11, which has been the result of years of carefulbreeding and selection in a comprehensive soybean breeding program.There are numerous steps in the development of any novel, desirablesoybean variety. Plant breeding begins with the analysis and definitionof problems and weaknesses of the current germplasm, the establishmentof program goals, and the definition of specific breeding objectives.The next step is selection of germplasm that possess the traits to meetthe program goals. The breeder's goal is to combine in a single varietyan improved combination of desirable traits from the parental germplasm.These important traits may include, but are not limited to: higher seedyield, resistance to diseases and/or insects, tolerance to droughtand/or heat, altered fatty acid profile(s), abiotic stress tolerance,improvements in compositional traits, and better agronomiccharacteristics.

These product development processes, which lead to the final step ofmarketing and distribution, can take from six to twelve years from thetime the first cross is made until the finished seed is delivered to thefarmer for planting. Therefore, development of new varieties is atime-consuming process that requires precise planning, efficient use ofresources, and a minimum of changes in direction.

Soybean (Glycine max) is an important and valuable field crop. Thus, acontinuing goal of soybean breeders is to develop stable, high yieldingsoybean varieties that are agronomically sound. The reasons for thisgoal are to maximize the amount of grain produced on the land used andto supply food for both animals and humans. To accomplish this goal, thesoybean breeder must select and develop soybean plants that have thetraits that result in superior varieties.

The soybean is the world's leading source of vegetable oil and proteinmeal. The oil extracted from soybeans is used for cooking oil,margarine, and salad dressings. Soybean oil is composed of saturated,monounsaturated, and polyunsaturated fatty acids. It has a typicalcomposition of 11% palmitic, 4% stearic, 25% oleic, 50% linoleic, and 9%linolenic fatty acid content (“Economic Implications of Modified SoybeanTraits Summary Report”, Iowa Soybean Promotion Board & American SoybeanAssociation Special Report 92S, May 1990). Changes in fatty acidcomposition for improved oxidative stability and nutrition are alsoimportant traits. Industrial uses for processed soybean oil includeingredients for paints, plastics, fibers, detergents, cosmetics, andlubricants. Soybean oil may be split, inter-esterified, sulfurized,epoxidized, polymerized, ethoxylated, or cleaved. Designing andproducing soybean oil derivatives with improved functionality,oliochemistry, is a rapidly growing field. The typical mixture oftriglycerides is usually split and separated into pure fatty acids,which are then combined with petroleum-derived alcohols or acids,nitrogen, sulfonates, chlorine, or with fatty alcohols derived from fatsand oils.

Soybean is also used as a food source for both animals and humans.Soybean is widely used as a source of protein for animal feeds forpoultry, swine, and cattle. During processing of whole soybeans, thefibrous hull is removed and the oil is extracted. The remaining soybeanmeal is a combination of carbohydrates and approximately 50% protein.

For human consumption soybean meal is made into soybean flour which isprocessed to protein concentrates used for meat extenders or specialtypet foods. Production of edible protein ingredients from soybean offersa healthy, less expensive replacement for animal protein in meats aswell as dairy-type products.

SUMMARY

A novel soybean variety, designated XB31E11 is provided. Also providedare the seeds of soybean variety XB31E11, cells from soybean varietyXB31E11, plants of soybean XB31E11, and plant parts of soybean varietyXB31E11. Methods provided include producing a soybean plant by crossingsoybean variety XB31E11 with another soybean plant, methods forintrogressing a transgenic, a mutant trait, and/or a native trait intosoybean variety XB31E11, methods for producing other soybean varietiesor plant parts derived from soybean variety XB31E11, and methods ofcharacterizing soybean variety XB31E11. Soybean seed, cells, plants,germplasm, breeding lines, varieties, and plant parts produced by thesemethods and/or derived from soybean variety XB31E11 are furtherprovided.

Definitions

Certain definitions used in the specification are provided below. Alsoin the examples which follow, a number of terms are used. In order toprovide a clear and consistent understanding of the specification andclaims, the following definitions are provided:

AERBLT=AWB=AERIAL WEB BLIGHT. Aerial web blight is caused by the fungusRhizoctonia solani, which can also cause seedling blight and root rot.Stems, flowers, pods, petioles, and leaves are susceptible to formationof lesions. Tolerance to Aerial Web Blight is rated on a scale of 1 to9, with a score of 1 being very susceptible, ranging up to a score of 9being tolerant. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

ALLELE. Any of one or more alternative forms of a genetic sequence. In adiploid cell or organism, the two alleles of a given sequence typicallyoccupy corresponding loci on a pair of homologous chromosomes.

ANTHESIS. The time of a flower's opening.

APHID ANTIBIOSIS. Aphid antibiosis is the ability of a variety to reducethe survival, growth, or reproduction of aphids that feed on it.Screening scores are based on the ability of the plant to decrease therate of aphid reproduction. Plants are compared to resistant andsusceptible check plants grown in the same experiment. Scores of1=susceptible, 3=below average, 5=average, 7=above average, and9=exceptional tolerance. Preliminary scores are reported as doubledigits, for example ‘55’ indicates a preliminary score of 5 on the scaleof 1 to 9.

APHID ANTIXENOSIS. Aphid antixenosis is a property of a variety toreduce the feeding of aphids upon the plant, this is also known asnonpreference. Screening scores are based on the ability of the plant todecrease the rate of aphid reproduction. Plants are compared toresistant and susceptible check plants grown in the same experiment.Scores of 1=susceptible plants covered with aphids, plants may showsevere damage such as stunting and/or necrosis, equivalent or worse whencompared to susceptible check, 3=below average, plants show major damagesuch as stunting and/or foliar necrosis, 5=moderately susceptible,7=above average, about 50 aphids on the plant, plant does not exhibitsigns of plant stress, and 9=exceptional tolerance, very few aphids onthe plant, equivalent or better when compared to a resistant check.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

BACKCROSSING. Process in which a breeder crosses a donor parent varietypossessing a desired trait or traits to a recurrent parent variety(which is agronomically superior but lacks the desired level or presenceof one or more traits) and then crosses the resultant progeny back tothe recurrent parent one or more times. Backcrossing can be used tointroduce one or more desired traits from one genetic background intoanother background that is lacking the desired traits.

BREEDING. The genetic manipulation of living organisms, includingapplication of agricultural and/or biotechnological tools, methodsand/or processes to create useful new distinct varieties.

BU/A=Bushels per Acre. The seed yield in bushels/acre is the actualyield of the grain at harvest.

BROWN STEM ROT=BSR=Brown Stem Rot Tolerance. This is a visual diseasescore from 1 to 9 comparing all genotypes in a given test. The score isbased on leaf symptoms of yellowing, necrosis, and on inner stem rottingcaused by Phialophora gregata. A score of 1 indicates severe symptoms ofleaf yellowing and necrosis. Increasing visual scores from 2 to 8indicate additional levels of tolerance, while a score of 9 indicates nosymptoms. Preliminary scores are reported as double digits, for example‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

BSRLF=Brown Stem Rot disease rating based solely on leaf diseasesymptoms. This is a visual disease score from 1 to 9 comparing allgenotypes in a given test. A score of 1 indicates severe leaf yellowingand necrosis. Increasing visual scores from 2 to 8 indicate additionallevels of tolerance, while a score of 9 indicates no leaf symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

BSRSTM=Brown Stem Rot disease rating based solely on stem diseasesymptoms. This is a visual disease score from 1 to 9 comparing allgenotypes in a given test. A score of 1 indicates severe necrosis on theinner stem tissues. Increasing visual scores from 2 to 8 indicateadditional levels of tolerance, while a score of 9 indicates no innerstem symptoms. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

CELL. Cell as used herein includes a plant cell, whether isolated, intissue culture, or incorporated in a plant or plant part.

CERK=CERCOSPORA TOLERANCE. A fungal disease caused by Cercosporakukuchii which can be identified by mottled purple-to-orangediscoloration of the uppermost leaves of the soybean plant. Infectedseeds typically have a purple discoloration, which is commonly referredto as purple seed stain. Plants are visually scored from 1 to 9comparing all genotypes in a given test. A score of 1 indicates severediscoloration of the leaves, while a score of 9 indicates no symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

CRDC=CHARCOAL ROT DISEASE. A fungal disease caused by Macrophominaphaseolina that is enhanced by hot and dry conditions, especially duringreproductive growth stages. Tolerance score is based on observations ofthe comparative ability to tolerate drought and limit losses fromcharcoal rot infection among various soybean varieties. A score of 1indicates severe charcoal rot on the roots and dark microsclerotia onthe lower stem. Increasing visual scores from 2 to 8 indicate additionallevels of tolerance, while a score of 9 indicates no lower stem and/orroot rot. Preliminary scores are reported as double digits, for example‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

CHLORIDE SENSITIVITY. This is a measure of the chloride concentration inthe plant tissue from 1 to 9. The higher the score the lower theconcentration of chloride in the tissue measured. Preliminary scores arereported as double digits, for example ‘55’ indicates a preliminaryscore of 5 on the scale of 1 to 9.

CW=Canopy Width. This is a visual observation of the canopy width whichis scored from 1 to 9 comparing all genotypes in a given test. A scoreof 1=very narrow, while a score of 9=very bushy.

CNKR=STEM CANKER TOLERANCE. This is a visual disease score from 1 to 9comparing all genotypes in a given field test. The score is based uponfield reaction to the disease. Two causative agents have beenidentified, Diaporthe phaseolorum var. caulivora, and Diaporthephaseolorum var. meridionalis, which tend to impact different geographicregions, with D. phaseolorum var. caulivora identified as the causativeagent for Northern stem canker, and D. phaseolorum var. meridionalisidentified as the causative agent for Southern stem canker. CNKSTindicates the tolerance score for Southern stem canker. A score of 1indicates susceptibility to the disease, whereas a score of 9 indicatesthe line is resistant to the disease. Preliminary scores are reported asdouble digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

CNKSG=STEM CANKER GENE. Resistance based on a specific gene that infersspecific resistance or susceptibility to a specific race of Stem Canker.The score is based upon a reaction of toothpick inoculation with a raceof stem canker. A score of 1 indicates severe stem canker lesions,similar to a known susceptible check variety, whereas a score of 9indicates no disease symptoms, consistent with a known resistant checkvariety. Preliminary scores are reported as double digits, for example‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

COTYLEDON. A cotyledon is a type of seed leaf. The cotyledon containsthe food storage tissues of the seed.

CROSS-POLLINATION. Fertilization by the union of two gametes fromdifferent plants.

DIPLOID. A cell or organism having two sets of chromosomes.

DM=DOWNY MILDEW. A fungal disease caused by Peronospora manshurica insoybean. Symptoms first appear on leaves, which can spread to podswithout obvious external symptoms, and further spread to seed. Infectedseed may have a dull white appearance. The tolerance score is based onobservations of symptoms on the leaves of plants regarding leaf damageand/or level of infection. On a scale of 1 to 9, a score of 1 indicatessevere symptoms, whereas a score of 9 indicates no disease symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

ELITE VARIETY. A variety that is sufficiently homozygous and homogeneousto be used for commercial grain production. An elite variety may also beused in further breeding.

EMBRYO. The embryo is the small plant contained within a mature seed.

EMGSC=Emergence Score=Field Emergence. A score based upon speed andstrength of emergence at sub-optimal conditions. Rating is done at theunifoliate to first trifoliate stages of growth. A score using a 1 to 9scale is given, with 1 being the poorest and 9 the best. Scores of 1, 2,and 3=degrees of unacceptable stands; slow growth and poor plant health.Scores of 4, 5, 6=degrees of less than optimal stands; moderate growthand plant health. Scores of 7, 8, 9=degrees of optimal stands; vigorousgrowth and plant health.

FEC=Iron-deficiency Chlorosis. Plants are scored 1 to 9 based on visualobservations. A score of 1 indicates the plants are dead or dying fromiron-deficiency chlorosis, a score of 5 means plants have intermediatehealth with some leaf yellowing, and a score of 9 means no stunting ofthe plants or yellowing of the leaves. Preliminary scores are reportedas double digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

FEY=FROGEYE LEAF SPOT. This is a visual fungal disease score from 1 to 9comparing all genotypes in a given experiment. The score is based uponthe number and size of leaf lesions. A score of 1 indicates severe leafnecrosis spotting, whereas a score of 9 indicates no lesions.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

FLOWER COLOR. Data values include: P=purple and W=white.

GENE SILENCING. The interruption or suppression of the expression of anucleic acid sequence at the level of transcription or translation.

GENOTYPE. Refers to the genetic constitution of a cell or organism.

PLANT HABIT. This refers to the physical appearance of a plant. It canbe determinate (Det), semi-determinate, intermediate, or indeterminate(Ind). In soybeans, indeterminate varieties are those in which stemgrowth is not limited by formation of a reproductive structure (i.e.,flowers, pods and seeds) and hence growth continues throughout floweringand during part of pod filling. The main stem will develop and set podsover a prolonged period under favorable conditions. In soybeans,determinate varieties are those in which stem growth ceases at floweringtime. Most flowers develop simultaneously, and most pods fill atapproximately the same time. The terms semi-determinate and intermediateare also used to describe plant habit and are defined in Bernard, R. L.(1972) “Two genes affecting stem termination in soybeans.” Crop Science12:235-239; Woodworth, C. M. (1932) “Genetics and breeding in theimprovement of the soybean.” Bull. Agric. Exp. Stn. (Illinois)384:297-404; and Woodworth, C. M. (1933) “Genetics of the Soybean.” J.Am. Soc. Agron. 25:36-51.

HAPLOID. A cell or organism having one set of the two sets ofchromosomes in a diploid cell or organism.

HERBRES=Herbicide Resistance. This indicates that the plant is moretolerant to the herbicide shown than the level of herbicide toleranceexhibited by wild type plants. A designation of ‘RR’ indicates toleranceto glyphosate, a designation of ‘GAT’ indicates tolerance to glyphosate,and a designation of ‘STS’ indicates tolerance to sulfonylureaherbicides.

HGT=Plant Height. Plant height is taken from the top of the soil to thetop pod of the plant and is measured in inches.

HILUM. This refers to the scar left on the seed which marks the placewhere the seed was attached to the pod prior to harvest. Hila Color datavalues include: BR=brown; TN=tan; Y=yellow; BL=black; IB=ImperfectBlack; BF=buff. Tan hila may also be designated as imperfect yellow(IY).

HYPL=Hypocotyl length=Hypocotyl elongation. This score indicates theability of the seed to emerge when planted 3″ deep in sand pots and witha controlled temperature of 25° C. The number of plants that emerge eachday are counted. Based on this data, each genotype is given a score from1 to 9 based on its rate of emergence and the percent of emergence. Ascore of 1 indicates a very poor rate and percent of emergence, anintermediate score of 5 indicates average ratings, and a score of 9indicates an excellent rate and percent of emergence.

HYPOCOTYL. A hypocotyl is the portion of an embryo or seedling betweenthe cotyledons and the root.

LDGSEV=Lodging Resistance=Harvest Standability. Lodging is rated on ascale of 1 to 9. A score of 1 indicates plants that are laying on theground, a score of 5 indicates plants are leaning at a 45° angle inrelation to the ground, and a score of 9 indicates erect plants.

LEAFLETS. These are parts of the plant shoot involved in the manufactureof food for the plant by the process of photosynthesis.

LINKAGE. Refers to a phenomenon wherein alleles on the same chromosometend to segregate together more often than expected by chance if theirtransmission was independent.

LINKAGE DISEQUILIBRIUM. Refers to a phenomenon wherein alleles tend toremain together in linkage groups when segregating from parents tooffspring, with a greater frequency than expected from their individualfrequencies.

LLC=Oil with three percent or less linolenic acid is classified as lowlinolenic oil. Linolenic acid is one of the five most abundant fattyacids in soybean seeds. It is measured by gas chromatography and isreported as a percent of the total oil content.

LLE=Linoleic Acid Percent. Linoleic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LLN=Linolenic Acid Percent. Linolenic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

LOCUS. A defined segment of DNA.

PRM=PRMMAT=Predicted Relative Maturity=RM=Relative Maturity. Soybeanmaturities are divided into relative maturity groups (00, 0, I, II, III,IV, . . . X or 00, 0, 1, 2, 3, . . . 10). Within a maturity group aresub-groups. A sub-group is a tenth of a relative maturity group (forexample 1.3 would indicate a group 1 and subgroup 3). Within narrowcomparisons, the difference of a tenth of a relative maturity groupequates very roughly to a day difference in maturity at harvest.

MAT ABS=ABSOLUTE MATURITY. This term is defined as the length of timefrom planting to complete physiological development (maturity). Theperiod from planting until maturity is reached is measured in days,usually in comparison to one or more standard varieties. Plants areconsidered mature when 95% of the pods have reached their mature color.

MATURITY GROUP. This refers to an agreed-on industry division of groupsof varieties, based on the zones in which they are adapted primarilyaccording to day length or latitude. They consist of very long daylength varieties (Groups 000, 00, 0), and extend to very short daylength varieties (Groups VII, VIII, IX, X).

NARROW ROWS. Term indicates 7″ and 15″ row spacing.

NEI DISTANCE. A quantitative measure of percent similarity between twolines. Nei's distance between lines A and B can be defined as1−((2*number alleles in common)/(number alleles in A+number alleles inB)). For example, if lines A and B are the same for 95 out of 100alleles, the Nei distance would be 0.05. If lines A and B are the samefor 98 out of 100 alleles, the Nei distance would be 0.02. Free softwarefor calculating Nei distance is available on the internet at multiplelocations such as, e.g., evolution.genetics.washington.edu/phylip.html.See Nei & Li (1979) Proc Natl Acad Sci USA 76:5269-5273, which isincorporated by reference for this purpose.

NUCLEIC ACID. An acidic, chainlike biological macromolecule consistingof multiple repeat units of phosphoric acid, sugar, and purine andpyrimidine bases.

OIL=OIL PERCENT=OIL (%). Soybean seeds contain a considerable amount ofoil. Oil is measured by NIR spectrophotometry and is reported as apercentage basis.

OIL/MEAL TYPE. Designates varieties specially developed with thefollowing oil traits: HLC=High Oleic oil; LLC=Low Linolenic (≦3%linolenic content); ULC=Ultra Low Linolenic oil (≦1% linolenic oilcontent); HSC=High Sucrose meal; LPA=Low Phytic Acid; LST=Low Saturateoil; Blank=Conventional variety/oil composition.

OLC=OLEIC ACID PERCENT. Oleic acid is one of the five most abundantfatty acids in soybean seeds. It is measured by gas chromatography andis reported as a percent of the total oil content.

PEDIGREE DISTANCE. Relationship among generations based on theirancestral links as evidenced in pedigrees. May be measured by thedistance of the pedigree from a given starting point in the ancestry.

PERCENT IDENTITY. Percent identity as used herein refers to thecomparison of the homozygous alleles of two soybean varieties. Percentidentity is determined by comparing a statistically significant numberof the homozygous alleles of two developed varieties. For example, apercent identity of 90% between soybean variety 1 and soybean variety 2means that the two varieties have the same allele at 90% of the lociused in the comparison.

PERCENT SIMILARITY. Percent similarity as used herein refers to thecomparison of the homozygous alleles of a soybean variety such asXB31E11 with another plant, and if the homozygous allele of XB31E11matches at least one of the alleles from the other plant, then they arescored as similar. Percent similarity is determined by comparing astatistically significant number of loci and recording the number ofloci with similar alleles as a percentage. A percent similarity of 90%between XB31E11 and another plant means that XB31E11 matches at leastone of the alleles of the other plant at 90% of the loci used in thecomparison.

PLANT. As used herein, the term “plant” includes reference to animmature or mature whole plant, including a plant from which seed orgrain or anthers have been removed. Seed or embryo that will produce theplant is also considered to be the plant.

PLANT PARTS. As used herein, the term “plant parts” includes leaves,stems, roots, root tips, anthers, seed, grain, embryos, pollen, ovules,flowers, cotyledon, hypocotyl, pod, flower, shoot, stalk, tissue, tissuecultures, cells and the like.

PLM or PALMITIC ACID PERCENT. Palmitic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

PMG infested soils. Soils containing Phytophthora sojae.

POD. This refers to the fruit of a soybean plant. It consists of thehull or shell (pericarp) and the soybean seeds. Pod Color data valuesinclude: BR=brown; TN=tan.

PRT or PHYTOPHTHORA FIELD TOLERANCE. Tolerance to Phytophthora root rotis rated on a scale of 1 to 9, with a score of 1 indicating the plantshave no tolerance to Phytophthora, ranging to a score of 9 being thebest or highest tolerance. PRTLAB indicates the tolerance was scoredusing plants in lab assay experiments. Preliminary scores are reportedas double digits, for example ‘55’ indicates a preliminary score of 5 onthe scale of 1 to 9.

PHYTOPHTHORA RESISTANCE GENE (Rps). Various Phytophthora resistancegenes are known and include but are not limited to: Rps1-a=resistance toraces 1-2, 10-11, 13-8, 24; Rps1-c=resistance to races 1-3, 6-11, 13,15, 17, 21, 23, 24, 26, 28-30, 32, 34, 36; Rps1-k=resistance to races1-11, 13-15, 17, 18, 21-24, 26, 36, 37; Rps3-a=resistance to races 1-5,8, 9, 11, 13, 14, 16, 18, 23, 25, 28, 29, 31-35, 39-41, 43-45, 47-52,54; Rps3-c=resistance to races 1-4, 10-16, 18-36, 38-54; Rps6=resistanceto races 1-4, 10, 12, 14-16, 18-21, 25, 28, 33-35; and, Rps8=resistanceto races 1-5, 9, 13-15, 21, 25, 29, 32. As reported in Table 1 “-” or “” indicates that a specific gene for resistance has not been identifiedto date.

PRO=PROTN=PROTN (%)=PROTEIN PERCENT. Soybean seeds contain aconsiderable amount of protein. Protein is generally measured by NIRspectrophotometry, and is reported as a percent on a dry weight basis.

PUBESCENCE. This refers to a covering of very fine hairs closelyarranged on the leaves, stems and pods of the soybean plant. Pubescencecolor data values include: L=Light Tawny; T=Tawny; G=Gray.

R160=Palmitic Acid percentage. Percentage of palmitic acid as determinedusing methods described in Reske et al. (1997) “TriacylglycerolComposition and Structure in Genetically Modified Sunflower and SoybeanOils” JAOCS 74:989-998, which is incorporated by reference for thispurpose.

R180=Stearic acid percentage. Percentage of Stearic acid as determinedusing methods described in Reske et al. (1997) JAOCS 74:989-998, whichis incorporated by reference for this purpose.

R181=Oleic acid percentage. Percentage of oleic acid as determined usingmethods described in Reske et al. (1997) JAOCS 74:989-998, which isincorporated by reference for this purpose.

R182=Linoleic acid percentage. Percentage of linoleic acid as determinedusing methods described in Reske et al. (1997) JAOCS 74:989-998, whichis incorporated by reference for this purpose.

R183=Linolenic acid percentage. Percentage of linolenic acid asdetermined using methods described in Reske et al. (1997) JAOCS74:989-998, which is incorporated by reference for this purpose.

RESISTANCE. As used herein, resistance is synonymous with tolerance andis used to describe the ability of a plant to withstand exposure to aninsect, disease, herbicide, environmental stress, or other condition. Aresistant plant variety will be able to better withstand the insect,disease pathogen, herbicide, environmental stress, or other condition ascompared to a non-resistant or wild-type variety.

RKI=ROOT-KNOT NEMATODE, Southern. Southern root knot nematode,Meloidogyne incognita, is a plant parasite that can cause major damage.Resistance is visually scored on a range from 1 to 9 comparing allgenotypes in a given experiment. The score is determined by diggingplants to visually score the roots for presence or absence of galling. Ascore of 1 indicates large severe galling covering most of the rootsystem which results in pre-mature death from decomposition of the rootsystem (susceptible). A score of 9 indicates that there is no galling ofthe roots (resistant). Preliminary scores are reported as double digits,for example ‘55’ indicates a preliminary score of 5 on the scale of 1 to9.

RKA=ROOT-KNOT NEMATODE, Peanut. Peanut root knot nematode, Meloidogynearenaria, is a plant parasite that can cause major damage. Resistance isvisually scored on a range from 1 to 9 comparing all genotypes in agiven experiment. This is a visual disease score from 1 to 9 comparingall genotypes in a given experiment. The score is determined by diggingplants to score the roots for presence or absence of galling. A score of1 indicates large severe galling covering most of the root system whichresults in pre-mature death from decomposition of the root system(susceptible). A score of 9 indicates that there is no galling of theroots (resistant). Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

SCN=SOYBEAN CYST NEMATODE RESISTANCE=Cyst Nematode Resistance. The scoreis based on resistance to a particular race of soybean cyst nematode(Heterodera glycines), such as race 1, 2, 3, 5 or 14. Scores are from 1to 9 and indicate visual observations of resistance as compared to othergenotypes in the test. A score of 1 indicates nematodes are able toinfect the plant and cause yield loss, while a score of 9 indicates SCNresistance. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

SCN Resistance Source. There are three typical sources of geneticresistance to SCN: PI88788, PI548402 (also known as Peking), andPI437654 (also known as Hartwig).

SCN infected soils. Soils containing soybean cyst nematode.

SD VIG or Seedling Vigor. The score is based on the speed of emergenceof the plants within a plot relative to other plots within anexperiment. A score of 1 indicates no plants have expanded first leaves,while a score of 9 indicates that 90% of plants growing have expandedfirst leaves.

SDS or SUDDEN DEATH SYNDROME. SDS is caused by the fungal pathogenformerly known as Fusarium solani fsp. glycines, which is currentlyknown as Fusarium virguliforme (see, e.g., Aoki et al. (2003) Mycologia95:660-684). Tolerance to Sudden Death Syndrome is rated on a scale of 1to 9, with a score of 1 being very susceptible ranging up to a score of9 being tolerant. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

SEED COAT LUSTER. Data values include D=dull; S=shiny.

SEED SIZE SCORE. This is a measure of the seed size from 1 to 9. Thehigher the score, the smaller the seed size measured.

SPLB=S/LB=Seeds per Pound. Soybean seeds vary in seed size, therefore,the number of seeds required to make up one pound also varies. Thisaffects the pounds of seed required to plant a given area, and can alsoimpact end uses.

SHATTR or Shattering. This refers to the amount of pod dehiscence priorto harvest. Pod dehiscence involves seeds falling from the pods to thesoil. This is a visual score from 1 to 9 comparing all genotypes withina given test. A score of 1 indicates 100% of the pods are opened, whilea score of 9 means pods have not opened and no seeds have fallen out.

SHOOTS. These are a portion of the body of the plant. They consist ofstems, petioles and leaves.

STC or Stearic Acid Percent. Stearic acid is one of the five mostabundant fatty acids in soybean seeds. It is measured by gaschromatography and is reported as a percent of the total oil content.

SUBLINE. Although XB31E11 contains substantially fixed genetics, and isphenotypically uniform and with no off-types expected, there stillremains a small proportion of segregating loci either within individualsor within the population as a whole.

WHMD or WHITE MOLD TOLERANCE. This is a fungal disease caused bySclerotinia sclerotiorum that creates mycelial growth and death ofplants. Tolerance to white mold is scored from 1 to 9 by visuallycomparing all genotypes in a given test. A score of 1 indicates completedeath of the experimental unit while a score of 9 indicates no symptoms.Preliminary scores are reported as double digits, for example ‘55’indicates a preliminary score of 5 on the scale of 1 to 9.

VARIETY. A substantially homozygous soybean line and minor modificationsthereof that retain the overall genetics of the soybean line includingbut not limited to a subline, a locus conversion, a mutation, atransgenic, or a somaclonal variant. Variety includes seeds, plants,plant parts, and/or seed parts of the instant soybean line.

HIGH YIELD ENVIRONMENTS. Areas which lack normal stress, typicallyhaving sufficient rainfall, water drainage, low disease pressure, andlow weed pressure.

TOUGH ENVIRONMENTS. Areas which have stress challenges, opposite of ahigh yield environment.

DETAILED DESCRIPTION

Soybean variety XB31E11 has shown uniformity and stability for alltraits, as described in the following variety description information.Soybean variety XB31E11 was developed from a cross of YB35R05 with92M81. Variety XB31E11 is an F3-derived line which was advanced to theF3 generation by modified single-seed descent. It has beenself-pollinated a sufficient number of generations, with carefulattention to uniformity of plant type to ensure a sufficient level ofhomozygosity and phenotypic stability. The variety has been increasedwith continued observation for uniformity. No variant traits have beenobserved or are expected.

A variety description of soybean variety XB31E11 is provided in Table 1.Traits reported are average values for all locations and years orsamples measured. Preliminary scores are reported as double digits, forexample ‘55’ indicates a preliminary score of 5 on the scale of 1 to 9.

Soybean variety XB31E11, being substantially homozygous, can bereproduced by planting seeds of the variety, growing the resultingsoybean plants under self-pollinating or sib-pollinating conditions, andharvesting the resulting seed, using techniques familiar to theagricultural arts. Development of soybean variety XB31E11 is shown inthe breeding history summary in Table 4.

Performance Examples of XB31E11

As shown in Table 2, the traits and characteristics of soybean varietyXB31E11 are given in paired comparisons with other varieties. Traitsreported are mean values for all locations and years where pairedcomparison data was obtained.

Genetic Marker Profile

In addition to phenotypic observations, a plant can also be identifiedby its genotype. The genotype of a plant can be characterized through agenetic marker profile which can identify plants of the same variety ora related variety, or which can be used to determine or validate apedigree. Genetic marker profiles can be obtained by techniques such asrestriction fragment length polymorphisms (RFLPs), randomly amplifiedpolymorphic DNAs (RAPDs), arbitrarily primed polymerase chain reaction(AP-PCR), DNA amplification fingerprinting (DAF), sequence characterizedamplified regions (SCARs), amplified fragment length polymorphisms(AFLPs), simple sequence repeats (SSRs) also referred to asmicrosatellites, or single nucleotide polymorphisms (SNPs). For example,see Cregan et al. (1999) “An Integrated Genetic Linkage Map of theSoybean Genome” Crop Science 39:1464-1490, and Berry et al. (2003)“Assessing Probability of Ancestry Using Simple Sequence RepeatProfiles: Applications to Maize Inbred Lines and Soybean Varieties”Genetics 165:331-342, each of which are incorporated by reference hereinin their entirety.

Methods of characterizing soybean variety XB31E11, or a varietycomprising the morphological and physiological characteristics ofsoybean variety XB31E11, are provided. In one example a methodcomprising isolating nucleic acids from a plant, a plant part, or a seedof soybean variety XB31E11, analyzing said nucleic acids to producedata, and recording the data for XB31E11 is provided. In some examples,the data is recorded on a computer readable medium. In other examples,the methods may further comprise using the data for soybean crossing,selection or advancement decisions. Crossing includes any type of plantbreeding crossing method, including but not limited to outcrossing,selfing, backcrossing, locus conversion, introgression and the like.

Particular markers used for these purposes are not limited to anyparticular set of markers, but are envisioned to include any type ofmarker and marker profile which provides a means of distinguishingvarieties. For example, one set of publicly available markers whichcould be used to screen and identify variety XB31E11 is disclosed inTable 3. In another example, one method of comparison is to use onlyhomozygous loci for XB31E11.

Primers and PCR protocols for assaying these and other markers aredisclosed in Soybase (sponsored by the USDA Agricultural ResearchService and Iowa State University) located on the world wide web at129.186.26.94/SSR.html. In addition to being used for identification ofsoybean variety XB31E11, and plant parts and plant cells of varietyXB31E11, the genetic profile may be used to identify a soybean plantproduced through the use of XB31E11 or to verify a pedigree for progenyplants produced through the use of XB31E11. The genetic marker profileis also useful in breeding and developing backcross conversions.

The present invention comprises a soybean plant characterized bymolecular and physiological data obtained from the representative sampleof said variety deposited with the American Type Culture Collection(ATCC). Thus, plants, seeds, or parts thereof, having all orsubstantially all of the physiological and morphological characteristicsof soybean variety XB31E11 are provided. Further provided is a soybeanplant formed by the combination of the disclosed soybean plant or plantcell with another soybean plant or cell and comprising the homozygousalleles of the variety. A soybean plant comprising all of thephysiological and morphological characteristics of soybean varietyXB31E11 can be combined with another soybean plant in a soybean breedingprogram. In some examples the other soybean plant comprises all of thephysiological and morphological characteristics of soybean varietyXB31E11.

In some examples, a plant, a plant part, or a seed of soybean varietyXB31E11 is characterized by producing a molecular profile. A molecularprofile includes but is not limited to one or more genotypic and/orphenotypic profile(s). A genotypic profile includes but is not limitedto a marker profile, such as a genetic map, a linkage map, a traitmarker profile, a SNP profile, an SSR profile, a genome-wide markerprofile, a haplotype, and the like. A molecular profile may also be anucleic acid sequence profile, and/or a physical map. A phenotypicprofile includes but is not limited to a protein expression profile, ametabolic profile, an mRNA expression profile, and the like.

Means of performing genetic marker profiles using SSR polymorphisms arewell known in the art. A marker system based on SSRs can be highlyinformative in linkage analysis relative to other marker systems in thatmultiple alleles may be present. Another advantage of this type ofmarker is that, through use of flanking primers, detection of SSRs canbe achieved, for example, by using the polymerase chain reaction (PCR),thereby eliminating the need for labor-intensive Southern hybridization.PCR detection is done using two oligonucleotide primers flanking thepolymorphic segment of repetitive DNA to amplify the SSR region.

Following amplification, markers can be scored by electrophoresis of theamplification products. Scoring of marker genotype is based on the sizeof the amplified fragment, which correlates to the number of base pairsof the fragment. While variation in the primer used or in laboratoryprocedures can affect the reported fragment size, relative values shouldremain constant regardless of the specific primer or laboratory used.When comparing varieties it is preferable if all SSR profiles areperformed in the same lab.

Primers used are publicly available and may be found in Soybase orCregan (1999 Crop Science 39:1464-1490). See also, WO 99/31964“Nucleotide Polymorphisms in Soybean”, U.S. Pat. No. 6,162,967“Positional Cloning of Soybean Cyst Nematode Resistance Genes”, and U.S.Pat. No. 7,288,386 “Soybean Sudden Death Syndrome Resistant Soybeans andMethods of Breeding and Identifying Resistant Plants”, the disclosuresof which are incorporated herein by reference.

The SSR profile of soybean plant XB31E11 can be used to identify plantscomprising XB31E11 as a parent, since such plants will comprise the samehomozygous alleles as XB31E11. Because the soybean variety isessentially homozygous at all relevant loci, most loci should have onlyone type of allele present. In contrast, a genetic marker profile of anF1 progeny should be the sum of those parents, e.g., if one parent washomozygous for allele X at a particular locus, and the other parenthomozygous for allele Y at that locus, then the F1 progeny will be XY(heterozygous) at that locus. Subsequent generations of progeny producedby selection and breeding are expected to be of genotype XX(homozygous), YY (homozygous), or XY (heterozygous) for that locusposition. When the F1 plant is selfed or sibbed for successive filialgenerations, the locus should be either X or Y for that position.

In addition, plants and plant parts substantially benefiting from theuse of XB31E11 in their development, such as XB31E11 comprising abackcross conversion, transgene, or genetic sterility factor, may beidentified by having a molecular marker profile with a high percentidentity to XB31E11. Such a percent identity might be 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 99.9% identical to XB31E11.

The SSR profile of variety XB31E11 also can be used to identifyessentially derived varieties and other progeny varieties developed fromthe use of XB31E11, as well as cells and other plant parts thereof.Plants of the invention include any plant having at least 90%, 91%, 92%,93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 99.9% of the markers in theSSR profile, and that retain 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, 99%, 99.5%, or 99.9% of the physiological and morphologicalcharacteristics of variety XB31E11 when grown under the same conditions.Such plants may be developed using the markers identified in WO00/31964, U.S. Pat. No. 6,162,967 and U.S. Pat. No. 7,288,386. Progenyplants and plant parts produced using XB31E11 may be identified byhaving a molecular marker profile of at least 25%, 30%, 35%, 40%, 45%,50%, 55%, 60%, 65%, 70%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%,84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%,98%, 99% or 99.5% genetic contribution from soybean variety XB31E11, asmeasured by either percent identity or percent similarity. Such progenymay be further characterized as being within a pedigree distance ofXB31E11, such as within 1, 2, 3, 4, or 5 or less cross-pollinations to asoybean plant other than XB31E11, or a plant that has XB31E11 as aprogenitor. Unique molecular profiles may be identified with othermolecular tools such as SNPs and RFLPs.

Introduction of a New Trait or Locus into XB31E11

Variety XB31E11 represents a new base genetic variety into which a newlocus or trait may be introgressed. Direct transformation andbackcrossing represent two important methods that can be used toaccomplish such an introgression.

A backcross conversion of XB31E11 occurs when DNA sequences areintroduced through backcrossing (Hallauer et al. in Corn and CornImprovement, Sprague and Dudley, Third Ed. 1998) with XB31E11 utilizedas the recurrent parent. Both naturally occurring and transgenic DNAsequences may be introduced through backcrossing techniques. A backcrossconversion may produce a plant with a trait or locus conversion in atleast two or more backcrosses, including at least 2 backcrosses, atleast 3 backcrosses, at least 4 backcrosses, at least 5 backcrosses, ormore. Molecular marker assisted breeding or selection may be utilized toreduce the number of backcrosses necessary to achieve the backcrossconversion. For example, see Openshaw et al., “Marker-assisted Selectionin Backcross Breeding”. In: Proceedings Symposium of the Analysis ofMolecular Data, August 1994, Crop Science Society of America, Corvallis,Oreg., which demonstrated that a backcross conversion can be made in asfew as two backcrosses.

The complexity of the backcross conversion method depends on the type oftrait being transferred (a single gene or closely linked genes comparedto unlinked genes), the level of expression of the trait, the type ofinheritance (cytoplasmic or nuclear), dominant or recessive traitexpression, and the types of parents included in the cross. It isunderstood by those of ordinary skill in the art that for single genetraits that are relatively easy to classify, the backcross method iseffective and relatively easy to manage. (See Hallauer et al., in Cornand Corn Improvement, Sprague and Dudley, Third Ed. 1998). Desiredtraits that may be transferred through backcross conversion include, butare not limited to, sterility (nuclear and cytoplasmic), fertilityrestoration, nutritional enhancements, drought tolerance, nitrogenutilization, altered fatty acid profile, low phytate, industrialenhancements, disease resistance (bacterial, fungal, or viral), insectresistance, and herbicide resistance. In addition, a recombination siteitself, such as an FRT site, Lox site, or other site specificintegration site, may be inserted by backcrossing and utilized fordirect insertion of one or more genes of interest into a specific plantvariety. A single locus may contain several transgenes, such as atransgene for disease resistance and a transgene for herbicideresistance. The gene for herbicide resistance may be used as aselectable marker and/or as a phenotypic trait. A single locusconversion of site specific integration system allows for theintegration of multiple genes at a known recombination site in thegenome.

The backcross conversion may result from either the transfer of adominant allele or a recessive allele. Selection of progeny containingthe trait of interest can be accomplished by direct selection for atrait associated with a dominant allele. Transgenes transferred viabackcrossing typically function as a dominant single gene trait and arerelatively easy to classify. Selection of progeny for a trait that istransferred via a recessive allele requires growing and selfing thefirst backcross generation to determine which plants carry the recessivealleles. Recessive traits may require additional progeny testing insuccessive backcross generations to determine the presence of the locusof interest. The last backcross generation is usually selfed to givepure breeding progeny for the trait(s) being transferred, although abackcross conversion with a stably introgressed trait may also bemaintained by further backcrossing to the recurrent parent withsubsequent selection for the trait.

Along with selection for the trait of interest, progeny are selected forthe phenotype of the recurrent parent. The backcross is a form ofinbreeding, and the features of the recurrent parent are automaticallyrecovered after successive backcrosses. Poehlman suggests from one tofour or more backcrosses, but as noted above, the number of backcrossesnecessary can be reduced with the use of molecular markers (Poehlman etal., (1995) Breeding Field Crops, 4th Ed., Iowa State University Press,Ames, Iowa). Other factors, such as a genetically similar donor parent,may also reduce the number of backcrosses necessary. As noted byPoehlman, backcrossing is easiest for simply inherited, dominant, andeasily recognized traits.

One process for adding or modifying a trait or locus in soybean varietyXB31E11 comprises crossing XB31E11 plants grown from XB31E11 seed withplants of another soybean plant that comprises a desired trait lackingin XB31E11, selecting F1 progeny plants that possess the desired traitor locus to produce selected F1 progeny plants, crossing the selectedprogeny plants back to XB31E11 plants to produce backcross) (BC1)progeny plants. The BC1F1 progeny plants that have the desired trait andthe morphological characteristics of soybean variety XB31E11 areselected and backcrossed to XB31E11 to generate BC2F1 progeny plants.Additional backcrossing and selection of progeny plants with the desiredtrait will produce BC3F1, BC4F1, BC5F1, . . . BCxF1 generations ofplants. The backcross populations of XB31E11 may be furthercharacterized as having the physiological and morphologicalcharacteristics of soybean variety XB31E11 listed in Table 1 asdetermined at the 5% significance level when grown in the sameenvironmental conditions and/or may be characterized by percentsimilarity or identity to XB31E11 as determined by SSR or othermolecular markers. The above method may be utilized with fewerbackcrosses in appropriate situations, such as when the donor parent ishighly related or molecular markers are used in one or more selectionsteps. Desired traits that may be used include those nucleic acids knownin the art, some of which are listed herein, that will affect traitsthrough nucleic acid expression or inhibition. Desired loci also includethe introgression of FRT, Lox, and/or other recombination sites for sitespecific integration. Desired loci further include QTLs, which may alsoaffect a desired trait.

In addition, the above process and other similar processes describedherein may be used to produce first generation progeny soybean seed byadding a step at the end of the process that comprises crossing XB31E11with the introgressed trait or locus with a different soybean plant andharvesting the resultant first generation progeny soybean seed.

Transgenes and transformation methods provide means to engineer thegenome of plants to contain and express heterologous genetic elements,including but not limited to foreign genetic elements, additional copiesof endogenous elements, and/or modified versions of native or endogenousgenetic elements, in order to alter at least one trait of a plant in aspecific manner that would be difficult or impossible to obtain withtraditional plant breeding alone. Any heterologous DNA sequence(s),whether from a different species or from the same species, which areinserted into the genome using transformation, backcrossing, or othermethods known to one of skill in the art are referred to hereincollectively as transgenes. The sequences are heterologous based onsequence source, location of integration, operably linked elements, orany combination thereof. One or more transgenes of interest can beintroduced into soybean variety XB31E11. Transgenic variants of soybeanvariety XB31E11 plants, seeds, cells, and parts thereof or derivedtherefrom are provided. Transgenic variants of XB31E11 comprise thephysiological and morphological characteristics of soybean varietyXB31E11 listed in Table 1 as determined at the 5% significance levelwhen grown in the same environmental conditions, and/or may becharacterized or identified by percent similarity or identity to XB31E11as determined by SSR or other molecular markers. In some examples,transgenic variants of soybean variety XB31E11 are produced byintroducing at least one transgene of interest into soybean varietyXB31E11 by transforming XB31E11 with a polynucleotide comprising thetransgene of interest. In other examples, transgenic variants of soybeanvariety XB31E11 are produced by introducing at least one transgene byintrogressing the transgene into soybean variety XB31E11 by crossing.

In one example, a process for modifying soybean variety XB31E11 with theaddition of a desired trait, said process comprising transforming asoybean plant of variety XB31E11 with a transgene that confers a desiredtrait is provided. Therefore, transgenic XB31E11 soybean cells, plants,plant parts, and seeds produced from this process are provided. In someexamples, the desired trait may be one or more of herbicide resistance,insect resistance, disease resistance, decreased phytate, modified fattyacid profile, modified fatty acid content, carbohydrate metabolism,protein content, or oil content. The specific gene may be any known inthe art or listed herein, including but not limited to a polynucleotideconferring resistance to imidazolinone, sulfonylurea, protoporphyrinogenoxidase (PPO) inhibitors, hydroxyphenyl pyruvate dioxygenase (H PPD)inhibitors, glyphosate, glufosinate, triazine, 2,4-dichlorophenoxyaceticacid (2,4-D), dicamba, or benzonitrile herbicides; a polynucleotideencoding a Bacillus thuringiensis polypeptide, a polynucleotide encodinga phytase, a fatty acid desaturase (e.g., FAD-2, FAD-3), galactinolsynthase, a raffinose synthetic enzyme; or a polynucleotide conferringresistance to soybean cyst nematode, brown stem rot, Phytophthora rootrot, soybean mosaic virus, sudden death syndrome, or other plantpathogen.

Numerous methods for plant transformation have been developed, includingbiological and physical plant transformation protocols. See, forexample, Miki et al., “Procedures for Introducing Foreign DNA intoPlants” in Methods in Plant Molecular Biology and Biotechnology, Glick,B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages67-88; and Armstrong (1999) “The First Decade of Maize Transformation: AReview and Future Perspective” Maydica 44:101-109. In addition,expression vectors and in vitro culture methods for plant cell or tissuetransformation and regeneration of plants are available. See, forexample, Gruber et al., “Vectors for Plant Transformation” in Methods inPlant Molecular Biology and Biotechnology, Glick, B. R. and Thompson, J.E. Eds. (CRC Press, Inc., Boca Raton, 1993) pages 89-119.

The most prevalent types of plant transformation methods involve theconstruction of an expression vector. Such a vector comprises a DNAsequence that contains a gene under the control of or operatively linkedto a regulatory element, for example a promoter. The vector may containone or more genes and one or more regulatory elements.

A genetic trait which has been engineered into the genome of aparticular soybean plant may then be moved into the genome of anothervariety using traditional breeding techniques that are well known in theplant breeding arts. For example, a backcrossing approach is commonlyused to move a transgene from a transformed soybean variety into anelite soybean variety, and the resulting backcross conversion plantwould then contain the transgene(s).

Various genetic elements can be introduced into the plant genome usingtransformation. These elements include, but are not limited to genes;coding sequences; inducible, constitutive, and tissue specificpromoters; enhancing sequences; and signal and targeting sequences.

Transgenic plants can be used to produce commercial quantities of aforeign protein. Thus, techniques for the selection and propagation oftransformed plants, which are well understood in the art, yield aplurality of transgenic plants that are harvested in a conventionalmanner, and a heterologous protein then can be extracted from a tissueof interest or from total biomass. Protein extraction from plant biomasscan be accomplished by known methods which are discussed, for example,by Heney and Orr (1981) Anal. Biochem. 114:92-6.

A genetic map can be generated that identifies the approximatechromosomal location of the integrated DNA molecule, for example viaconventional restriction fragment length polymorphisms (RFLP),polymerase chain reaction (PCR) analysis, simple sequence repeats (SSR),and single nucleotide polymorphisms (SNP). For exemplary methodologiesin this regard, see Glick and Thompson, Methods in Plant MolecularBiology and Biotechnology, pp. 269-284 (CRC Press, Boca Raton, 1993).

Wang et al. discuss “Large Scale Identification, Mapping and Genotypingof Single-Nucleotide Polymorphisms in the Human Genome”, Science (1998)280:1077-1082, and similar capabilities are increasingly available forthe soybean genome. Map information concerning chromosomal location isuseful for proprietary protection of a subject transgenic plant. Ifunauthorized propagation is undertaken and crosses made with othergermplasm, the map of the integration region can be compared to similarmaps for suspect plants to determine if the latter have a commonparentage with the subject plant. Map comparisons could involvehybridizations, RFLP, PCR, SSR, sequencing or combinations thereof, allof which are conventional techniques. SNPs may also be used alone or incombination with other techniques.

Likewise, plants can be genetically engineered to express variousphenotypes of agronomic interest. Through the transformation of soybeanthe expression of genes can be altered to enhance disease resistance,insect resistance, herbicide resistance, agronomic, grain quality, andother traits. Transformation can also be used to insert DNA sequenceswhich control or help control male-sterility. DNA sequences native tosoybean as well as non-native DNA sequences can be transformed intosoybean and used to alter levels of native or non-native proteins.Various promoters, targeting sequences, enhancing sequences, and otherDNA sequences can be inserted into the genome for the purpose ofaltering the expression of proteins. Reduction of the activity ofspecific genes (also known as gene silencing or gene suppression) isdesirable for several aspects of genetic engineering in plants.

Many techniques for gene silencing are well known to one of skill in theart, including but not limited to, knock-outs (such as by insertion of atransposable element such as mu (Vicki Chandler, The Maize Handbook ch.118 (Springer-Verlag 1994); antisense technology (see, e.g., Sheehy etal. (1988) PNAS USA 85:8805-8809; and U.S. Pat. Nos. 5,107,065;5,453,566; and 5,759,829); co-suppression (e.g., Taylor (1997) PlantCell 9:1245; Jorgensen (1990) Trends Biotech. 8:340-344; Flavell (1994)PNAS USA 91:3490-3496; Finnegan et al. (1994) Bio/Technology 12:883-888;and Neuhuber et al. (1994) Mol. Gen. Genet. 244:230-241); RNAinterference (Napoli et al. (1990) Plant Cell 2:279-289; U.S. Pat. No.5,034,323; Sharp (1999) Genes Dev. 13:139-141; Zamore et al. (2000) Cell101:25-33; and Montgomery et al. (1998) PNAS USA 95:15502-15507);virus-induced gene silencing (Burton et al. (2000) Plant Cell12:691-705; and Baulcombe (1999) Curr. Op. Plant Biol. 2:109-113);target-RNA-specific ribozymes (Haseloff et al. (1988) Nature 334:585-591); hairpin structures (Smith et al. (2000) Nature 407:319-320; WO99/53050; and WO 98/53083); microRNA (Aukerman & Sakai (2003) Plant Cell15:2730-2741); ribozymes (Steinecke et al. (1992) EMBO J. 11:1525; andPerriman et al. (1993) Antisense Res. Dev. 3:253); oligonucleotidemediated targeted modification (e.g., WO 03/076574 and WO 99/25853);Zn-finger targeted molecules (e.g., WO 01/52620; WO 03/048345; and WO00/42219); and other methods or combinations of the above methods knownto those of skill in the art.

Exemplary nucleotide sequences that may be altered by geneticengineering include, but are not limited to, those categorized below.

1. Transgenes that Confer Resistance to Insects or Disease and thatEncode:

(A) Plant disease resistance genes. Plant defenses are often activatedby specific interaction between the product of a disease resistance gene(R) in the plant and the product of a corresponding avirulence (Avr)gene in the pathogen. A plant variety can be transformed with clonedresistance gene to engineer plants that are resistant to specificpathogen strains. See, for example Jones et al. (1994) Science 266: 789(cloning of the tomato Cf-9 gene for resistance to Cladosporium fulvum);Martin et al. (1993) Science 262:1432 (tomato Pto gene for resistance toPseudomonas syringae pv. tomato encodes a protein kinase); Mindrinos etal. (1994) Cell 78:1089 (Arabidopsis RPS2 gene for resistance toPseudomonas syringae), McDowell & Woffenden (2003) Trends Biotechnol.21:178-83; and Toyoda et al. (2002) Transgenic Res. 11:567-82. A plantresistant to a disease is one that is more resistant to a pathogen ascompared to the wild type plant.

(B) A Bacillus thuringiensis (Bt) protein, a derivative thereof or asynthetic polypeptide modeled thereon. See, for example, Geiser et al.(1986) Gene 48:109, who disclose the cloning and nucleotide sequence ofa Bt delta-endotoxin gene. Moreover, DNA molecules encodingdelta-endotoxin genes can be purchased from American Type CultureCollection (Rockville, Md.), for example, under ATCC Accession Nos.40098, 67136, 31995, and 31998. Other non-limiting examples of Bacillusthuringiensis transgenes being genetically engineered are given in thefollowing patents and patent applications, and hereby are incorporatedby reference for this purpose: U.S. Pat. Nos. 5,188,960; 5,689,052;5,880,275; 5,986,177; 7,105,332; 7,208,474; WO 91/14778; WO 99/31248; WO01/12731; WO 99/24581; WO 97/40162; US2002/0151709; US2003/0177528;US2005/0138685; US/20070245427; US2007/0245428; US2006/0241042;US2008/0020966; US2008/0020968; US2008/0020967; US2008/0172762;US2008/0172762; and US2009/0005306.

(C) An insect-specific hormone or pheromone such as an ecdysteroid orjuvenile hormone, a variant thereof, a mimetic based thereon, or anantagonist or agonist thereof. See, for example, the disclosure byHammock et al. (1990) Nature 344:458, of baculovirus expression ofcloned juvenile hormone esterase, an inactivator of juvenile hormone.

(D) An insect-specific peptide which peptide, upon expression, disruptsthe physiology of the affected pest. For example, see the disclosures ofRegan (1994) J. Biol. Chem. 269:9 (expression cloning yields DNA codingfor insect diuretic hormone receptor); Pratt et al. (1989) Biochem.Biophys. Res. Comm. 163:1243 (an allostatin is identified in Diplopterapuntata); Chattopadhyay et al. (2004) Critical Reviews in Microbiology30:33-54 2004; Zjawiony (2004) J Nat Prod 67:300-310; Carlini &Grossi-de-Sa (2002) Toxicon 40:1515-1539; Ussuf et al. (2001) Curr Sci.80:847-853; and Vasconcelos & Oliveira (2004) Toxicon 44:385-403. Seealso U.S. Pat. No. 5,266,317 to Tomalski et al., who disclose genesencoding insect-specific toxins.

(E) An enzyme responsible for a hyperaccumulation of a monoterpene, asesquiterpene, a steroid, hydroxamic acid, a phenylpropanoid derivative,or another non-protein molecule with insecticidal activity.

(F) An enzyme involved in the modification, including thepost-translational modification, of a biologically active molecule; forexample, a glycolytic enzyme, a proteolytic enzyme, a lipolytic enzyme,a nuclease, a cyclase, a transaminase, an esterase, a hydrolase, aphosphatase, a kinase, a phosphorylase, a polymerase, an elastase, achitinase and a glucanase, whether natural or synthetic. See WO93/02197, which discloses the nucleotide sequence of a callase gene. DNAmolecules which contain chitinase-encoding sequences can be obtained,for example, from the ATCC under Accession Nos. 39637 and 67152. Seealso Kramer et al. (1993) Insect Biochem. Molec. Biol. 23:691, who teachthe nucleotide sequence of a cDNA encoding tobacco hookworm chitinase,and Kawalleck et al. (1993) Plant Mol. Biol. 21:673, who provide thenucleotide sequence of the parsley ubi4-2 polyubiquitin gene, and U.S.Pat. Nos. 6,563,020; 7,145,060; and 7,087,810.

(G) A molecule that stimulates signal transduction. For example, see thedisclosure by Botella et al. (1994) Plant Mol. Biol. 24:757, ofnucleotide sequences for mung bean calmodulin cDNA clones, and Griess etal. (1994) Plant Physiol. 104:1467, who provide the nucleotide sequenceof a maize calmodulin cDNA clone.

(H) A hydrophobic moment peptide. See WO 95/16776 and U.S. Pat. No.5,580,852 disclosure of peptide derivatives of tachyplesin which inhibitfungal plant pathogens, and WO 95/18855 and U.S. Pat. No. 5,607,914which teach synthetic antimicrobial peptides that confer diseaseresistance.

(I) A membrane permease, a channel former, or a channel blocker. Forexample, see the disclosure by Jaynes et al. (1993) Plant Sci. 89:43, ofheterologous expression of a cecropin-beta lytic peptide analog torender transgenic tobacco plants resistant to Pseudomonas solanacearum.

(J) A viral-invasive protein or a complex toxin derived therefrom. Forexample, the accumulation of viral coat proteins in transformed plantcells imparts resistance to viral infection and/or disease developmenteffected by the virus from which the coat protein gene is derived, aswell as by related viruses. See Beachy et al. (1990) Ann. Rev.Phytopathol. 28:451. Coat protein-mediated resistance has been conferredupon transformed plants against alfalfa mosaic virus, cucumber mosaicvirus, tobacco streak virus, potato virus X, potato virus Y, tobaccoetch virus, tobacco rattle virus, and tobacco mosaic virus.

(K) An insect-specific antibody or an immunotoxin derived therefrom.Thus, an antibody targeted to a critical metabolic function in theinsect gut would inactivate an affected enzyme, killing the insect. Cf.Taylor et al., Abstract #497, Seventh Intl Symposium on MolecularPlant-Microbe Interactions (Edinburgh, Scotland, 1994) (enzymaticinactivation in transgenic tobacco via production of single-chainantibody fragments).

(L) A virus-specific antibody. See, for example, Tavladoraki et al.(1993) Nature 366:469, who show that transgenic plants expressingrecombinant antibody genes are protected from virus attack.

(M) A developmental-arrestive protein produced in nature by a pathogenor a parasite. Thus, fungal endo alpha-1,4-D-polygalacturonasesfacilitate fungal colonization and plant nutrient release bysolubilizing plant cell wall homo-alpha-1,4-D-galacturonase. See Lamb etal. (1992) Bio/Technology 10:1436. The cloning and characterization of agene which encodes a bean endopolygalacturonase-inhibiting protein isdescribed by Toubart et al. (1992) Plant J. 2:367.

(N) A developmental-arrestive protein produced in nature by a plant. Forexample, Logemann et al. (1992) Bio/Technology 10:305, have shown thattransgenic plants expressing the barley ribosome-inactivating gene havean increased resistance to fungal disease.

(O) Genes involved in the systemic acquired resistance (SAR) Responseand/or the pathogenesis related genes. Briggs (1995) Current Biology5:128-131, Pieterse & Van Loon (2004) Curr. Opin. Plant Bio. 7:456-64;and Somssich (2003) Cell 113:815-6.

(P) Antifungal genes (Cornelissen and Melchers (1993) Plant Physiol.101:709-712; Parijs et al. (1991) Planta 183:258-264; Bushnell et al.(1998) Can. J. Plant Path. 20:137-149. Also, see US2002/0166141;US2007/0274972; US2007/0192899; US2008/0022426; and U.S. Pat. Nos.6,891,085; 7,306,946; and 7,598,346.

(Q) Detoxification genes, such as for fumonisin, beauvericin,moniliformin, zearalenone, and their structurally related derivatives.For example, see U.S. Pat. Nos. 5,716,820; 5,792,931; 5,798,255;5,846,812; 6,083,736; 6,538,177; 6,388,171; and 6,812,380.

(R) Cystatin and cysteine proteinase inhibitors. See U.S. Pat. No.7,205,453.

(S) Defensin genes. See WO 03/000863 and U.S. Pat. Nos. 6,911,577;6,855,865; 6,777,592; and 7,238,781.

(T) Genes conferring resistance to nematodes. See e.g. WO 96/30517; WO93/19181; WO 03/033651; and Urwin et al. (1998) Planta 204:472-479;Williamson (1999) Curr Opin Plant Bio. 2:327-31; and U.S. Pat. Nos.6,284,948 and 7,301,069.

(U) Genes that confer resistance to Phytophthora Root Rot, such as Rps1,Rps1-a, Rps1-b, Rps1-c, Rps1-d, Rps1-e, Rps1-k, Rps2, Rps3-a, Rps3-b,Rps3-c, Rps4, Rps5, Rps6, Rps7, Rps8, and other Rps genes. See, forexample, Shoemaker et al. “Phytophthora Root Rot Resistance Gene Mappingin Soybean”, Plant Genome IV Conference, San Diego, Calif. (1995).

(V) Genes that confer resistance to Brown Stem Rot, such as described inU.S. Pat. No. 5,689,035, and incorporated by reference for this purpose.

2. Transgenes that Confer Resistance to a Herbicide, for Example:

(A) A herbicide that inhibits the growing point or meristem, such as animidazolinone, or a sulfonylurea. Exemplary genes include mutant ALS andAHAS enzymes as described, for example, by Lee et al. (1988) EMBO J.7:1241; and, Miki et al. (1990) Theor. Appl. Genet. 80:449,respectively. See also, U.S. Pat. Nos. 5,605,011; 5,013,659; 5,141,870;5,767,361; 5,731,180; 5,304,732; 4,761,373; 5,331,107; 5,928,937; and5,378,824; US2007/0214515; and WO 96/33270.

(B) Glyphosate (resistance imparted by mutant5-enolpyruv1-3-phosphikimate synthase (EPSP) and aroA genes,respectively) and other phosphono compounds such as glufosinate(phosphinothricin acetyl transferase (PAT) and Streptomyceshygroscopicus phosphinothricin acetyl transferase (bar) genes), andpyridinoxy or phenoxy proprionic acids and cyclohexones (ACCaseinhibitor-encoding genes). See, for example, U.S. Pat. No. 4,940,835 toShah et al., which discloses the nucleotide sequence of a form of EPSPSwhich can confer glyphosate resistance. U.S. Pat. No. 5,627,061 to Barryet al. also describes genes encoding EPSPS enzymes. See also U.S. Pat.Nos. 6,566,587; 6,338,961; 6,248,876; 6,040,497; 5,804,425; 5,633,435;5,145,783; 4,971,908; 5,312,910; 5,188,642; 4,940,835; 5,866,775;6,225,114; 6,130,366; 5,310,667; 4,535,060; 4,769,061; 5,633,448;5,510,471; RE 36,449; RE 37,287; and 5,491,288; and. EP1173580; WO01/66704; EP1173581; and EP1173582, which are incorporated herein byreference for this purpose. Glyphosate resistance is also imparted toplants that express a gene that encodes a glyphosate oxido-reductaseenzyme as described more fully in U.S. Pat. Nos. 5,776,760 and5,463,175, which are incorporated herein by reference for this purpose.In addition, glyphosate resistance can be imparted to plants by theoverexpression of genes encoding glyphosate N-acetyltransferase. See,for example, US2004/0082770; US2005/0246798; and US2008/0234130 whichare incorporated herein by reference for this purpose. A DNA moleculeencoding a mutant aroA gene can be obtained under ATCC accession No.39256, and the nucleotide sequence of the mutant gene is disclosed inU.S. Pat. No. 4,769,061 to Comai. European Patent Application No. 0 333033 to Kumada et al. and U.S. Pat. No. 4,975,374 to Goodman et al.disclose nucleotide sequences of glutamine synthetase genes which conferresistance to herbicides such as L-phosphinothricin. The nucleotidesequence of a phosphinothricin-acetyl-transferase gene is provided inEuropean Patent No. 0 242 246 and 0 242 236 to Leemans et al. De Greefet al. (1989) Bio/Technology 7:61 describe the production of transgenicplants that express chimeric bar genes coding for phosphinothricinacetyl transferase activity. See also, U.S. Pat. Nos. 5,969,213;5,489,520; 5,550,318; 5,874,265; 5,919,675; 5,561,236; 5,648,477;5,646,024; 6,177,616; and 5,879,903, which are incorporated herein byreference for this purpose. Exemplary genes conferring resistance tophenoxy proprionic acids and cyclohexones, such as sethoxydim andhaloxyfop, are the Acc1-S1, Acc1-S2, and Acc1-S3 genes described byMarshall et al. (1992) Theor. Appl. Genet. 83:435.

(C) A herbicide that inhibits photosynthesis, such as a triazine (psbAand gs+ genes) and a benzonitrile (nitrilase gene). Przibilla et al.(1991) Plant Cell 3:169, describe the transformation of Chlamydomonaswith plasmids encoding mutant psbA genes. Nucleotide sequences fornitrilase genes are disclosed in U.S. Pat. No. 4,810,648 to Stalker, andDNA molecules containing these genes are available under ATCC AccessionNos. 53435, 67441, and 67442. Cloning and expression of DNA coding for aglutathione S-transferase is described by Hayes et al. (1992) Biochem.J. 285:173.

(D) Acetohydroxy acid synthase, which has been found to make plants thatexpress this enzyme resistant to multiple types of herbicides, has beenintroduced into a variety of plants (see, e.g., Hattori et al. (1995)Mol Gen Genet. 246:419). Other genes that confer resistance toherbicides include: a gene encoding a chimeric protein of rat cytochromeP4507A1 and yeast NADPH-cytochrome P450 oxidoreductase (Shiota et al.(1994) Plant Physiol 106:17), genes for glutathione reductase andsuperoxide dismutase (Aono et al. (1995) Plant Cell Physiol 36:1687),and genes for various phosphotransferases (Datta et al. (1992) Plant MolBiol 20:619).

(E) Protoporphyrinogen oxidase (protox) is necessary for the productionof chlorophyll, which is necessary for all plant survival. The protoxenzyme serves as the target for a variety of herbicidal compounds. Theseherbicides also inhibit growth of all the different species of plantspresent, causing their total destruction. The development of plantscontaining altered protox activity which are resistant to theseherbicides are described in U.S. Pat. Nos. 6,288,306; 6,282,837; and5,767,373; and WO 01/12825.

3. Transgenes that Confer or Contribute to a Grain and/or SeedCharacteristic, Such as:

(A) Fatty acid profile(s), for example, by

-   -   (1) Down-regulation of stearoyl-ACP desaturase to increase        stearic acid content of the plant. See Knultzon et al. (1992)        Proc. Natl. Acad. Sci. USA 89:2624; and WO 99/64579 (Genes for        Desaturases to Alter Lipid Profiles in Corn).    -   (2) Elevating oleic acid via FAD-2 gene modification and/or        decreasing linolenic acid via FAD-3 gene modification (see U.S.        Pat. Nos. 6,063,947; 6,323,392; 6,372,965; and WO 93/11245).    -   (3) Altering conjugated linolenic or linoleic acid content, such        as in WO 01/12800.    -   (4) Altering LEC1, AGP, Dek1, Superal1, mi1ps, various Ipa genes        such as Ipa1, Ipa3, hpt or hggt. For example, see WO 02/42424;        WO 98/22604; WO 03/011015; U.S. Pat. Nos. 6,423,886; 6,197,561;        and, 6,825,397; US2003/0079247; US2003/0204870; WO 02/057439; WO        03/011015; and Rivera-Madrid et al. (1995) Proc. Natl. Acad.        Sci. 92:5620-5624.

B) Altered Phosphorus Content, for Example, by:

-   -   (1) Introduction of a phytase-encoding gene would enhance        breakdown of phytate, adding more free phosphate to the        transformed plant. For example, see Van Hartingsveldt et        al. (1993) Gene 127:87, for a disclosure of the nucleotide        sequence of an Aspergillus niger phytase gene.    -   (2) Modulating a gene that reduces phytate content. In maize,        this, for example, could be accomplished, by cloning and then        re-introducing DNA associated with one or more of the alleles,        such as the LPA alleles, identified in maize mutants        characterized by low levels of phytic acid, such as in WO        05/113778; and/or by altering inositol kinase activity as in WO        02/059324; U.S. Pat. No. 7,067,720; WO 03/027243;        US2003/0079247; WO 99/05298; U.S. Pat. Nos. 6,197,561;        6,291,224; and 6,391,348; WO 98/45448; WO 99/55882; and WO        01/04147.

(C) Altered carbohydrates, for example, by altering a gene for an enzymethat affects the branching pattern of starch or, a gene alteringthioredoxin such as NTR and/or TRX (see U.S. Pat. No. 6,531,648 which isincorporated by reference for this purpose) and/or a gamma zein knockoutor mutant such as cs27, or TUSC27, or en27 (See U.S. Pat. No. 6,858,778;US2005/0160488; and US2005/0204418; which are incorporated by referencefor this purpose). See Shiroza et al. (1988) J. Bacteriol. 170:810(nucleotide sequence of Streptococcus mutans fructosyltransferase gene);Steinmetz et al. (1985) Mol. Gen. Genet. 200:220 (nucleotide sequence ofBacillus subtilis levansucrase gene); Pen et al. (1992) Bio/Technology10:292 (production of transgenic plants that express Bacilluslichenifonnis alpha-amylase); Elliot et al. (1993) Plant Mol. Biol.21:515 (nucleotide sequences of tomato invertase genes); Søgaard et al.(1993) J. Biol. Chem. 268:22480 (site-directed mutagenesis of barleyalpha-amylase gene); Fisher et al. (1993) Plant Physiol. 102:1045 (maizeendosperm starch branching enzyme II); WO 99/10498 (improveddigestibility and/or starch extraction through modification ofUDP-D-xylose 4-epimerase, Fragile 1 and 2, Reft HCHL, C4H); and, U.S.Pat. No. 6,232,529 (method of producing high oil seed by modification ofstarch levels (AGP). The fatty acid modification genes mentioned hereinmay also be used to affect starch content and/or composition through theinterrelationship of the starch and oil pathways.

(D) Altered antioxidant content or composition, such as alteration oftocopherol or tocotrienols. For example, see U.S. Pat. Nos. 6,787,683;7,154,029; and WO 00/68393 involving the manipulation of antioxidantlevels, and WO 03/082899 through alteration of a homogentisate geranylgeranyl transferase (hggt).

(E) Altered essential seed amino acids. For example, see U.S. Pat. No.6,127,600 (method of increasing accumulation of essential amino acids inseeds); U.S. Pat. No. 6,080,913 (binary methods of increasingaccumulation of essential amino acids in seeds); U.S. Pat. No. 5,990,389(high lysine); WO 99/40209 (alteration of amino acid compositions inseeds); WO 99/29882 (methods for altering amino acid content ofproteins); U.S. Pat. No. 5,850,016 (alteration of amino acidcompositions in seeds); WO 98/20133 (proteins with enhanced levels ofessential amino acids); U.S. Pat. No. 5,885,802 (high methionine); U.S.Pat. No. 5,885,801 (high threonine); U.S. Pat. No. 6,664,445 (plantamino acid biosynthetic enzymes); U.S. Pat. No. 6,459,019 (increasedlysine and threonine); U.S. Pat. No. 6,441,274 (plant tryptophansynthase beta subunit); U.S. Pat. No. 6,346,403 (methionine metabolicenzymes); U.S. Pat. No. 5,939,599 (high sulfur); U.S. Pat. No. 5,912,414(increased methionine); WO 98/56935 (plant amino acid biosyntheticenzymes); WO 98/45458 (engineered seed protein having higher percentageof essential amino acids); WO 98/42831 (increased lysine); U.S. Pat. No.5,633,436 (increasing sulfur amino acid content); U.S. Pat. No.5,559,223 (synthetic storage proteins with defined structure containingprogrammable levels of essential amino acids); WO 96/01905 (increasedthreonine); WO 95/15392 (increased lysine); U.S. Pat. Nos. 6,930,225;7,179,955; 6,803,498; US2004/0068767; and WO 01/79516.

4. Genes that Control Male-Sterility

There are several methods of conferring genetic male sterilityavailable, such as multiple mutant genes at separate locations withinthe genome that confer male sterility, as disclosed in U.S. Pat. Nos.4,654,465 and 4,727,219 to Brar et al. and chromosomal translocations asdescribed by Patterson in U.S. Pat. Nos. 3,861,709 and 3,710,511. Inaddition to these methods, Albertsen et al. U.S. Pat. No. 5,432,068,describe a system of nuclear male sterility which includes: identifyinga gene which is critical to male fertility; silencing this native genewhich is critical to male fertility; removing the native promoter fromthe essential male fertility gene and replacing it with an induciblepromoter; inserting this genetically engineered gene back into theplant; and thus creating a plant that is male sterile because theinducible promoter is not “on” resulting in the male fertility gene notbeing transcribed. Fertility is restored by inducing, or turning “on”,the promoter, which in turn allows the gene that confers male fertilityto be transcribed. Male sterile soybean lines and characterization arediscussed in Palmer (2000) Crop Sci 40:78-83, and Jin et al. (1997) SexPlant Reprod 10:13-21.

(A) Introduction of a deacetylase gene under the control of atapetum-specific promoter and with the application of the chemicalN-Ac-PPT (WO 01/29237).

(B) Introduction of various stamen-specific promoters (WO 92/13956 andWO 92/13957).

(C) Introduction of the barnase and the barstar gene (Paul et al. (1992)Plant Mol. Biol. 19:611-622).

For additional examples of nuclear male and female sterility systems andgenes, see also, U.S. Pat. Nos. 5,859,341; 6,297,426; 5,478,369;5,824,524; 5,850,014; and 6,265,640; all of which are herebyincorporated by reference.

5. Polynucleotides comprising a site for site specific DNArecombination. This includes the introduction of at least one FRT sitethat may be used in the FLP/FRT system and/or a Lox site that may beused in the Cre/Lox system. For example, see Lyznik et al. (2003) PlantCell Rep 21:925-932; and WO 99/25821, which are hereby incorporated byreference. Other systems that may be used include the Gin recombinase ofphage Mu (Maeser et al. (1991) Mol Gen Genet. 230:170-176); the Pinrecombinase of E. coli (Enomoto et al. (1983) J Bacteriol 156:663-668);and the R/RS system of the pSRi plasmid (Araki et al. (1992) J Mol Biol182:191-203).6. Genes that affect abiotic stress resistance (including but notlimited to flowering, ear, and seed development, enhancement of nitrogenutilization efficiency, altered nitrogen responsiveness, droughtresistance or tolerance, cold resistance or tolerance, and saltresistance or tolerance) and increased yield under stress. For example,see WO 00/73475 where water use efficiency is altered through alterationof malate; U.S. Pat. Nos. 5,892,009; 5,965,705; 5,929,305; 5,891,859;6,417,428; 6,664,446; 6,706,866; 6,717,034; and 6,801,104; WO 00/060089;WO 01/026459; WO 00/1035725; WO 01/034726; WO 01/035727; WO 00/1036444;WO 01/036597; WO 01/036598; WO 00/2015675; WO 02/017430; WO 02/077185;WO 02/079403; WO 03/013227; WO 03/013228; WO 03/014327; WO 04/031349; WO04/076638; WO 98/09521; and WO 99/38977 describing genes, including CBFgenes and transcription factors effective in mitigating the negativeeffects of freezing, high salinity, and drought on plants, as well asconferring other positive effects on plant phenotype; US2004/0148654 andWO 01/36596 where abscisic acid is altered in plants resulting inimproved plant phenotype such as increased yield and/or increasedtolerance to abiotic stress; WO 00/006341, WO 04/090143, U.S. Pat. Nos.7,531,723, and 6,992,237 where cytokinin expression is modifiedresulting in plants with increased stress tolerance, such as droughttolerance, and/or increased yield. Also see WO 02/02776, WO 03/052063,JP2002281975, U.S. Pat. No. 6,084,153, WO 01/64898, U.S. Pat. No.6,177,275, and U.S. Pat. No. 6,107,547 (enhancement of nitrogenutilization and altered nitrogen responsiveness). For ethylenealteration, see US2004/0128719, US2003/0166197, and WO 00/32761. Forplant transcription factors or transcriptional regulators of abioticstress, see e.g. US2004/0098764 or US2004/0078852.

Other genes and transcription factors that affect plant growth andagronomic traits such as yield, flowering, plant growth, and/or plantstructure, can be introduced or introgressed into plants, see e.g., WO97/49811 (LHY), WO 98/56918 (ESD4), WO 97/10339, and U.S. Pat. No.6,573,430 (TFL), U.S. Pat. No. 6,713,663 (FT), WO 96/14414 (CON), WO96/38560, WO 01/21822 (VRN1), WO 00/44918 (VRN2), WO 99/49064 (GI), WO00/46358 (FR1), WO 97/29123, U.S. Pat. No. 6,794,560, U.S. Pat. No.6,307,126 (GAI), WO 99/09174 (D8 and Rht), and WO 04/076638 and WO04/031349 (transcription factors).

Development of Soybean Sublines

Sublines of XB31E11 may also be developed and are provided. AlthoughXB31E11 contains substantially fixed genetics and is phenotypicallyuniform with no off-types expected, there still remains a smallproportion of segregating loci either within individuals or within thepopulation as a whole. Sublining provides the ability to select forthese loci, which have no apparent morphological or phenotypic effect onthe plant characteristics, but may have an effect on overall yield. Forexample, the methods described in U.S. Pat. No. 5,437,697 andUS2005/0071901 (each of which is herein incorporated by reference) maybe utilized by a breeder of ordinary skill in the art to identifygenetic loci that are associated with yield potential to further purifythe variety in order to increase its yield. A breeder of ordinary skillin the art may fix agronomically important loci by making themhomozygous in order to optimize the performance of the variety. Thedevelopment of soybean sublines and the use of accelerated yieldtechnology is a plant breeding technique.

Soybean varieties such as XB31E11 are typically developed for use inseed and grain production. However, soybean varieties such as XB31E11also provide a source of breeding material that may be used to developnew soybean varieties. Plant breeding techniques known in the art andused in a soybean plant breeding program include, but are not limitedto, recurrent selection, mass selection, bulk selection, backcrossing,pedigree breeding, open pollination breeding, restriction fragmentlength polymorphism enhanced selection, genetic marker enhancedselection, making double haploids, and transformation. Oftencombinations of these techniques are used. The development of soybeanvarieties in a plant breeding program requires, in general, thedevelopment and evaluation of homozygous varieties. There are manyanalytical methods available to evaluate a new variety. The oldest andmost traditional method of analysis is the observation of phenotypictraits but genotypic analysis may also be used.

Methods for producing a soybean plant by crossing a first parent soybeanplant with a second parent soybean plant wherein the first and/or secondparent soybean plant is variety XB31E11 are provided. Also provided aremethods for producing a soybean plant having substantially all of themorphological and physiological characteristics of variety XB31E11, bycrossing a first parent soybean plant with a second parent soybean plantwherein the first and/or the second parent soybean plant is a planthaving substantially all of the morphological and physiologicalcharacteristics of variety XB31E11 set forth in Table 1, as determinedat the 5% significance level when grown in the same environmentalconditions. The other parent may be any soybean plant, such as a soybeanplant that is part of a synthetic or natural population. Any suchmethods using soybean variety XB31E11 include but are not limited to:selfing, sibbing, backcrossing, mass selection, pedigree breeding, bulkselection, hybrid production, crossing to populations, and the like.These methods are well known in the art and some of the more commonlyused breeding methods are described below. Descriptions of breedingmethods can be found in one of several reference books (e.g., Allard,Principles of Plant Breeding, 1960; Simmonds, Principles of CropImprovement, 1979; Fehr, “Breeding Methods for Cultivar Development”,Chapter 7, Soybean Improvement, Production and Uses, 2^(nd) ed., Wilcoxeditor, 1987).

Pedigree breeding starts with the crossing of two genotypes, such asXB31E11 or a soybean variety having all of the morphological andphysiological characteristics of XB31E11, and another soybean varietyhaving one or more desirable characteristics that is lacking or whichcomplements XB31E11. If the two original parents do not provide all thedesired characteristics, other sources can be included in the breedingpopulation. In the pedigree method, superior plants are selfed andselected in successive filial generations. In the succeeding filialgenerations, the heterozygous allele condition gives way to thehomozygous allele condition as a result of inbreeding. Typically in thepedigree method of breeding, five or more successive filial generationsof selfing and selection are practiced: e.g., F1→F2; F2→F3; F3→F4;F4→F5; etc. In some examples, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or moregenerations of selfing and selection are practiced. After a sufficientamount of inbreeding, successive filial generations will serve toincrease seed of the developed variety. Typically, the developed varietycomprises homozygous alleles at about 95% or more of its loci.

In addition to being used to create backcross conversion populations,backcrossing can also be used in combination with pedigree breeding. Asdiscussed previously, backcrossing can be used to transfer one or morespecifically desirable traits from one variety (the donor parent) to adeveloped variety (the recurrent parent), which has good overallagronomic characteristics yet may lack one or more other desirabletraits. However, the same procedure can be used to move the progenytoward the genotype of the recurrent parent but at the same time retainmany components of the non-recurrent parent by stopping the backcrossingat an early stage and proceeding with selfing and selection. Forexample, a soybean variety may be crossed with another variety toproduce a first generation progeny plant. The first generation progenyplant may then be backcrossed to one of its parent varieties to create aBC1F1. Progeny are selfed and selected so that the newly developedvariety has many of the attributes of the recurrent parent and yetseveral of the desired attributes of the donor parent. This approachleverages the value and strengths of both parents for use in new soybeanvarieties.

Therefore, in some examples a method of making a backcross conversion ofsoybean variety XB31E11, comprising the steps of crossing a plant ofsoybean variety XB31E11 or a soybean variety having all of themorphological and physiological characteristics of XB31E11 with a donorplant possessing a desired trait to introduce the desired trait,selecting an F1 progeny plant containing the desired trait, andbackcrossing the selected F1 progeny plant to a plant of soybean varietyXB31E11 are provided. This method may further comprise the step ofobtaining a molecular marker profile of soybean variety XB31E11 andusing the molecular marker profile to select for a progeny plant withthe desired trait and the molecular marker profile of XB31E11. Themolecular marker profile can comprise information from one or moremarkers. In one example the desired trait is a mutant gene or transgenepresent in the donor parent. In another example, the desired trait is anative trait in the donor parent.

Recurrent selection is a method used in a plant breeding program toimprove a population of plants. Variety XB31E11, and/or a soybeanvariety having all of the morphological and physiologicalcharacteristics of XB31E11, is suitable for use in a recurrent selectionprogram. The method entails individual plants cross pollinating witheach other to form progeny. The progeny are grown and the superiorprogeny selected by any number of selection methods, which includeindividual plant, half-sib progeny, full-sib progeny, and selfedprogeny. The selected progeny are cross pollinated with each other toform progeny for another population. This population is planted and,again, superior plants are selected to cross pollinate with each other.Recurrent selection is a cyclical process and therefore can be repeatedas many times as desired. The objective of recurrent selection is toimprove the traits of a population. The improved population can then beused as a source of breeding material to obtain new varieties forcommercial or breeding use, including the production of a syntheticcultivar. A synthetic cultivar is the resultant progeny formed by theintercrossing of several selected varieties.

Mass selection is a useful technique when used in conjunction withmolecular marker enhanced selection. In mass selection, seeds fromindividuals are selected based on phenotype or genotype. These selectedseeds are then bulked and used to grow the next generation. Bulkselection requires growing a population of plants in a bulk plot,allowing the plants to self-pollinate, harvesting the seed in bulk, andthen using a sample of the seed harvested in bulk to plant the nextgeneration. Also, instead of self pollination, directed pollinationcould be used as part of the breeding program.

Mutation breeding is another method of introducing new traits intosoybean variety XB31E11 or a soybean variety having all of themorphological and physiological characteristics of XB31E11. Mutationsthat occur spontaneously or that are artificially induced can be usefulsources of variability for a plant breeder. The goal of artificialmutagenesis is to increase the rate of mutation for a desiredcharacteristic. Mutation rates can be increased by many different meansincluding temperature, long-term seed storage, tissue cultureconditions, radiation; such as X-rays, gamma rays (e.g., cobalt 60 orcesium 137), neutrons, (product of nuclear fission by uranium 235 in anatomic reactor), beta radiation (emitted from radioisotopes such asphosphorus 32 or carbon 14), ultraviolet radiation (preferably from 2500to 2900 nm), or chemical mutagens such as base analogues(5-bromo-uracil), related compounds (8-ethoxy caffeine), antibiotics(streptonigrin), alkylating agents (sulfur mustards, nitrogen mustards,epoxides, ethylenamines, sulfates, sulfonates, sulfones, lactones),azide, hydroxylamine, nitrous acid, or acridines. Once a desired traitis observed through mutagenesis, the trait may then be incorporated intoexisting germplasm by traditional breeding techniques. Details ofmutation breeding can be found in “Principles of Cultivar Development”Fehr, 1993, Macmillan Publishing Company. In addition, mutations createdin other soybean plants may be used to produce a backcross conversion ofXB31E11 that comprises such mutation.

Molecular markers, which include markers identified through the use oftechniques such as isozyme electrophoresis, restriction fragment lengthpolymorphisms (RFLPs), randomly amplified polymorphic DNAs (RAPDs),arbitrarily primed polymerase chain reaction (AP-PCR), DNA amplificationfingerprinting (DAF), sequence characterized amplified regions (SCARs),amplified fragment length polymorphisms (AFLPs), simple sequence repeats(SSRs), and single nucleotide polymorphisms (SNPs), may be used in plantbreeding methods utilizing XB31E11.

Isozyme electrophoresis and RFLPs have been widely used to determinegenetic composition. Shoemaker and Olsen (“Molecular Linkage Map ofSoybean (Glycine max L. Merr.)”, p. 6.131-6.138. In S. J. O'Brien (ed.)Genetic Maps: Locus Maps of Complex Genomes. (1993) Cold Spring HarborLaboratory Press. Cold Spring Harbor, N.Y.), developed a moleculargenetic linkage map that consisted of 25 linkage groups with about 365RFLP, 11 RAPD (random amplified polymorphic DNA), three classicalmarkers, and four isozyme loci. See also, Shoemaker “RFLP Map ofSoybean”. pp 299-309 (1994). In R. L. Phillips and I. K. Vasil (ed.)DNA-based markers in plants. Kluwer Academic Press Dordrecht, theNetherlands.

SSR technology is an efficient and practical marker technology; moremarker loci can be routinely used and more alleles per marker locus canbe found using SSRs in comparison to RFLPs. For example, Diwan andCregan, described a highly polymorphic microsatellite loci in soybeanwith as many as 26 alleles. (Diwan and Cregan (1997) Theor. Appl. Genet.95:220-225). Single nucleotide polymorphisms (SNPs) may also be used toidentify the unique genetic composition of the XB31E11 and progenyvarieties retaining or derived from that unique genetic composition.Various molecular marker techniques may be used in combination toenhance overall resolution.

Soybean DNA molecular marker linkage maps have been rapidly constructedand widely implemented in genetic studies. One such study is describedin Cregan et al. (1999) Crop Science 39:1464-1490. Sequences and PCRconditions of SSR loci in soybean, as well as the most current geneticmap, may be found in Soybase on the world wide web.

One use of molecular markers is quantitative trait loci (QTL) mapping.QTL mapping is the use of markers which are known to be closely linkedto alleles that have measurable effects on a quantitative trait.Selection in the breeding process is based upon the accumulation ofmarkers linked to the positive effecting alleles and/or the eliminationof the markers linked to the negative effecting alleles from the plantgenome.

Molecular markers can also be used during the breeding process for theselection of qualitative traits. For example, markers closely linked toalleles or markers containing sequences within the actual alleles ofinterest can be used to select plants that contain the alleles ofinterest during a backcrossing breeding program. The markers can also beused to select for the genome of the recurrent parent and against thegenome of the donor parent. Using this procedure can minimize the amountof genome from the donor parent that remains in the selected plants. Itcan also be used to reduce the number of crosses back to the recurrentparent needed in a backcrossing program. The use of molecular markers inthe selection process is often called genetic marker enhanced selection.

Production of Double Haploids

The production of double haploids can also be used for the developmentof plants with a homozygous phenotype in the breeding program. Forexample, a soybean plant for which variety XB31E11 or a soybean varietyhaving all of the morphological and physiological characteristics ofXB31E11 is a parent can be used to produce double haploid plants. Doublehaploids are produced by the doubling of a set of chromosomes (1 N) froma heterozygous plant to produce a completely homozygous individual. Forexample, see Wan et al., “Efficient Production of Doubled Haploid PlantsThrough Colchicine Treatment of Anther-Derived Maize Callus” (1989)Theor Appl Genet. 77:889-892, and US2003/0005479. This can beadvantageous because the process omits the generations of selfing neededto obtain a homozygous plant from a heterozygous source.

Methods for obtaining haploid plants are disclosed in Kobayashi et al.(1980) J Heredity 71:9-14; Pollacsek (1992) Agronomie (Paris)12:247-251; Cho-Un-Haing et al. (1996) J Plant Biol. 39:185-188;Verdoodt et al. (1998) Theor Appl Genet. 96:294-300; GeneticManipulation in Plant Breeding, Proceedings International SymposiumOrganized by EUCARPIA, Sep. 8-13, 1985, Berlin, Germany; Chalyk et al.(1994) Maize Genet Coop. Newsletter 68:47. Double haploid technology insoybean is discussed in Croser et al. (2006) Crit. Rev Plant Sci25:139-157; and Rodrigues et al. (2006) Brazilian Arc Biol Tech49:537-545.

In some examples a process for making a substantially homozygous XB31E11progeny plant by producing or obtaining a seed from the cross of XB31E11and another soybean plant and applying double haploid methods to the F1seed or F1 plant or to any successive filial generation is provided.Based on studies in maize, and currently being conducted in soybean,such methods would decrease the number of generations required toproduce a variety with similar genetics or characteristics to XB31E11.See Bernardo and Kahler (2001) Theor. Appl. Genet. 102:986-992.

In particular, a process of making seed retaining the molecular markerprofile of soybean variety XB31E11 is contemplated, such processcomprising obtaining or producing F1 seed for which soybean varietyXB31E11 is a parent, inducing doubled haploids to create progeny withoutthe occurrence of meiotic segregation, obtaining the molecular markerprofile of soybean variety XB31E11, and selecting progeny that retainthe molecular marker profile of XB31E11.

Methods using seeds, plants, cells, or plant parts of variety XB31E11 intissue culture are provided, as are the cultures, plants, parts, cells,and/or seeds derived therefrom. Tissue culture of various tissues ofsoybeans and regeneration of plants therefrom is well known and widelypublished. For example, see Komatsuda et al. (1991) Crop Sci.31:333-337; Stephens et al. “Agronomic Evaluation ofTissue-Culture-Derived Soybean Plants” (1991) Theor. Appl. Genet.82:633-635; Komatsuda et al. “Maturation and Germination of SomaticEmbryos as Affected by Sucrose and Plant Growth Regulators in SoybeansGlycine gracilis Skvortz and Glycine max (L.) Merr.” (1992) Plant CellTissue and Organ Culture 28:103-113; Dhir et al. “Regeneration ofFertile Plants from Protoplasts of Soybean (Glycine max L. Merr.):Genotypic Differences in Culture Response” (1992) Plant Cell Reports11:285-289; Pandey et al. “Plant Regeneration from Leaf and HypocotylExplants of Glycine wightii (W. and A.) VERDC. var. longicauda” (1992)Japan J. Breed. 42:1-5; and Shetty et al. “Stimulation of In Vitro ShootOrganogenesis in Glycine max (Merrill.) by Allantoin and Amides” (1992)Plant Science 81:245-251; U.S. Pat. No. 5,024,944, to Collins et al.;and U.S. Pat. No. 5,008,200, to Ranch et al., the disclosures of whichare hereby incorporated herein in their entirety by reference. Thus,another aspect is to provide cells which upon growth and differentiationproduce soybean plants having the physiological and morphologicalcharacteristics of soybean variety XB31E11.

DEPOSITS

Applicant made a deposit of seeds of Soybean Variety XB31E11 with theAmerican Type Culture Collection (ATCC), Manassas, Va. 20110 USA, ATCCDeposit No. PTA-11648. The seeds deposited with the ATCC on Feb. 2, 2011were taken from the seed stock maintained by Pioneer Hi-BredInternational, Inc., 7250 NW 62nd Avenue, Johnston, Iowa 50131 sinceprior to the filing date of this application. Access to this seed stockwill be available during the pendency of the application to theCommissioner of Patents and Trademarks and persons determined by theCommissioner to be entitled thereto upon request. Upon allowance of anyclaims in the application, the Applicant will make the deposit availableto the public pursuant to 37 C.F.R. §1.808. This deposit of SoybeanVariety XB31E11 will be maintained in the ATCC depository, which is apublic depository, for a period of 30 years, or 5 years after the mostrecent request, or for the enforceable life of the patent, whichever islonger, and will be replaced if it becomes nonviable during that period.Additionally, Applicant has or will satisfy all the requirements of 37C.F.R. §§1.801-1.809, including providing an indication of the viabilityof the sample upon deposit. Applicant has no authority to waive anyrestrictions imposed by law on the transfer of biological material orits transportation in commerce. Applicant does not waive anyinfringement of their rights granted under this patent or under thePlant Variety Protection Act (7 USC 2321 et seq.).

All publications, patents, and patent applications mentioned in thespecification are indicative of the level of those skilled in the art towhich this invention pertains. All such publications, patents, andpatent applications are incorporated by reference herein for the purposecited to the same extent as if each was specifically and individuallyindicated to be incorporated by reference herein.

The foregoing invention has been described in detail by way ofillustration and example for purposes of clarity and understanding. Asis readily apparent to one skilled in the art, the foregoing are onlysome of the methods and compositions that illustrate the embodiments ofthe foregoing invention. It will be apparent to those of ordinary skillin the art that variations, changes, modifications, and alterations maybe applied to the compositions and/or methods described herein withoutdeparting from the true spirit, concept, and scope of the invention.

TABLE 1 Variety Description Information Variety Name XB31E11 RelativeMaturity 3.1 Canadian Heat Units 3300 Herbicide Resistance RR HarvestStandability 8 Field Emergence 8 Hypocotyl Length Phytophthora Gene 1KPhytophthora Field Tolerance 4 Brown Stem Rot 6 Iron DeficiencyChlorosis 5 White Mold Tolerance 5 Sudden Death Syndrome 7 Cyst NematodeRace 1 Cyst Nematode Race 2 Cyst Nematode Race 3 88 Cyst Nematode Race 5Cyst Nematode Race 14 66 Root-knot Nematode - Southern Root-knotNematode - Peanut Stem Canker Genetic Stem Canker Tolerance AphidAntibiosis Cercospora Downy Mildew Frogeye Leaf Spot 99 ChlorideSensitivity Canopy Width 6 Shattering 88 Plant Habit Ind Oil/Meal TypeSeed Protein (% @ 13% H20) 34.3 Seed Oil (% @ 13% H20) 18.6 Seed SizeRange Flower Color W Pubescence Color L Hila Color BL Pod Color BR SeedCoat Luster D

TABLE 2 VARIETY COMPARISON DATA YIELD MAT HGT Variety1 Variety2Statistic bu/a (days) (in) LDGSEV XB31E11 93Y02 Mean1 60.4 121.3 37.87.8 XB31E11 93Y02 Mean2 57.7 120.5 35.5 8.5 XB31E11 93Y02 #Locs 26 8 4 2XB31E11 93Y02 #Reps 50 13 7 3 XB31E11 93Y02 #Years 1 1 1 1 XB31E11 93Y02SE Diff 1.14 0.42 0.97 0.75 XB31E11 93Y02 Prob 0.0251 0.1192 0.1027 0.5XB31E11 93Y03 Mean1 60.4 121.3 37.8 7.8 XB31E11 93Y03 Mean2 59 120.235.4 6.3 XB31E11 93Y03 #Locs 26 8 4 2 XB31E11 93Y03 #Reps 51 13 7 3XB31E11 93Y03 #Years 1 1 1 1 XB31E11 93Y03 SE Diff 1.12 0.45 1.09 0.5XB31E11 93Y03 Prob 0.2104 0.0493 0.1169 0.2048 XB31E11 93Y11 Mean1 61124.6 38.3 7.6 XB31E11 93Y11 Mean2 57.9 123.5 36.9 7.4 XB31E11 93Y11#Locs 45 16 8 4 XB31E11 93Y11 #Reps 70 21 11 5 XB31E11 93Y11 #Years 2 22 2 XB31E11 93Y11 SE Diff 0.7 0.65 1.06 0.63 XB31E11 93Y11 Prob 0.00010.1341 0.2338 0.7177 XB31E11 93Y13 Mean1 61 124.6 38.3 7.6 XB31E11 93Y13Mean2 58.9 124.3 36.7 7.6 XB31E11 93Y13 #Locs 45 16 8 4 XB31E11 93Y13#Reps 69 21 11 5 XB31E11 93Y13 #Years 2 2 2 2 XB31E11 93Y13 SE Diff 0.980.5 0.84 0.41 XB31E11 93Y13 Prob 0.0433 0.6705 0.1041 1 XB31E11 93Y20Mean1 61 124.6 38.3 7.6 XB31E11 93Y20 Mean2 59.4 124 40.4 6.8 XB31E1193Y20 #Locs 45 16 8 4 XB31E11 93Y20 #Reps 70 21 11 5 XB31E11 93Y20#Years 2 2 2 2 XB31E11 93Y20 SE Diff 0.8 0.54 1 0.66 XB31E11 93Y20 Prob0.0638 0.2876 0.0649 0.2754 XB31E11 RJS31004 Mean1 60.4 121.3 37.8 7.8XB31E11 RJS31004 Mean2 55.7 122.8 38.9 6.3 XB31E11 RJS31004 #Locs 26 8 42 XB31E11 RJS31004 #Reps 51 13 7 3 XB31E11 RJS31004 #Years 1 1 1 1XB31E11 RJS31004 SE Diff 0.86 0.63 1.05 0.5 XB31E11 RJS31004 Prob 00.0499 0.3618 0.2048 XB31E11 RJS34001 Mean1 60.4 121.3 37.8 7.8 XB31E11RJS34001 Mean2 60.2 123.8 40.9 6 XB31E11 RJS34001 #Locs 26 8 4 2 XB31E11RJS34001 #Reps 51 13 7 3 XB31E11 RJS34001 #Years 1 1 1 1 XB31E11RJS34001 SE Diff 0.96 0.42 0.83 0.25 XB31E11 RJS34001 Prob 0.7943 0.00050.0324 0.0903 SPLB PROTN Variety1 Variety2 Statistic count FEC SDS (%)XB31E11 93Y02 Mean1 3484 5.1 7.8 34.35 XB31E11 93Y02 Mean2 3667 2.9 5.634.48 XB31E11 93Y02 #Locs 3 3 3 5 XB31E11 93Y02 #Reps 5 7 8 8 XB31E1193Y02 #Years 1 1 1 1 XB31E11 93Y02 SE Diff 90.3 1.39 0.4 0.111 XB31E1193Y02 Prob 0.1803 0.2515 0.031 0.3079 XB31E11 93Y03 Mean1 3484 5.1 7.834.35 XB31E11 93Y03 Mean2 3428 4.2 6.1 34.17 XB31E11 93Y03 #Locs 3 3 3 5XB31E11 93Y03 #Reps 5 7 8 8 XB31E11 93Y03 #Years 1 1 1 1 XB31E11 93Y03SE Diff 87.4 0.48 0.4 0.194 XB31E11 93Y03 Prob 0.5874 0.2079 0.04720.4242 XB31E11 93Y11 Mean1 3211 5 7.4 34.44 XB31E11 93Y11 Mean2 3140 3.47.4 35.28 XB31E11 93Y11 #Locs 4 8 4 10 XB31E11 93Y11 #Reps 6 17 15 13XB31E11 93Y11 #Years 2 2 2 2 XB31E11 93Y11 SE Diff 86.3 0.36 0.49 0.252XB31E11 93Y11 Prob 0.4738 0.0039 0.9061 0.0086 XB31E11 93Y13 Mean1 32115.1 7.4 34.44 XB31E11 93Y13 Mean2 3432 3.1 5.1 33.48 XB31E11 93Y13 #Locs4 3 4 11 XB31E11 93Y13 #Reps 6 7 15 14 XB31E11 93Y13 #Years 2 1 2 2XB31E11 93Y13 SE Diff 95.9 1.15 0.51 0.336 XB31E11 93Y13 Prob 0.10410.2254 0.0214 0.0171 XB31E11 93Y20 Mean1 3211 5.1 7.4 34.46 XB31E1193Y20 Mean2 3342 5.3 6.9 33.8 XB31E11 93Y20 #Locs 4 3 4 9 XB31E11 93Y20#Reps 6 7 15 12 XB31E11 93Y20 #Years 2 1 2 2 XB31E11 93Y20 SE Diff 84.21.06 0.47 0.18 XB31E11 93Y20 Prob 0.2172 0.8534 0.3999 0.0062 XB31E11RJS31004 Mean1 3484 5.1 7.8 34.37 XB31E11 RJS31004 Mean2 3733 3.8 734.06 XB31E11 RJS31004 #Locs 3 3 3 6 XB31E11 RJS31004 #Reps 5 7 7 9XB31E11 RJS31004 #Years 1 1 1 1 XB31E11 RJS31004 SE Diff 42.7 0.33 0.440.146 XB31E11 RJS31004 Prob 0.0282 0.0572 0.1994 0.0906 XB31E11 RJS34001Mean1 3484 5.1 7.8 34.37 XB31E11 RJS34001 Mean2 3465 4.7 6.6 34 XB31E11RJS34001 #Locs 3 3 3 6 XB31E11 RJS34001 #Reps 5 7 8 9 XB31E11 RJS34001#Years 1 1 1 1 XB31E11 RJS34001 SE Diff 79.9 0.4 0.22 0.259 XB31E11RJS34001 Prob 0.8296 0.3828 0.0315 0.2117 OIL R160 R180 R181 Variety1Variety2 Statistic (%) (%) (%) (%) XB31E11 93Y02 Mean1 19.04 11.25 3.923.58 XB31E11 93Y02 Mean2 18.79 10.92 4.25 21.6 XB31E11 93Y02 #Locs 5 33 3 XB31E11 93Y02 #Reps 8 5 5 5 XB31E11 93Y02 #Years 1 1 1 1 XB31E1193Y02 SE Diff 0.176 0.093 0.1 0.164 XB31E11 93Y02 Prob 0.2314 0.06950.0728 0.0068 XB31E11 93Y03 Mean1 19.04 11.25 3.9 23.58 XB31E11 93Y03Mean2 19.51 10.52 3.72 23.73 XB31E11 93Y03 #Locs 5 3 3 3 XB31E11 93Y03#Reps 8 6 6 6 XB31E11 93Y03 #Years 1 1 1 1 XB31E11 93Y03 SE Diff 0.1420.044 0.073 0.475 XB31E11 93Y03 Prob 0.0287 0.0036 0.1276 0.7822 XB31E1193Y11 Mean1 18.36 11.25 3.9 23.58 XB31E11 93Y11 Mean2 18.58 10.63 4.0723.68 XB31E11 93Y11 #Locs 10 3 3 3 XB31E11 93Y11 #Reps 13 6 6 6 XB31E1193Y11 #Years 2 1 1 1 XB31E11 93Y11 SE Diff 0.165 0.067 0.044 0.785XB31E11 93Y11 Prob 0.209 0.0115 0.0634 0.9103 XB31E11 93Y13 Mean1 18.4311.25 3.9 23.58 XB31E11 93Y13 Mean2 18.86 9.83 4.3 25.22 XB31E11 93Y13#Locs 11 3 3 3 XB31E11 93Y13 #Reps 14 6 6 6 XB31E11 93Y13 #Years 2 1 1 1XB31E11 93Y13 SE Diff 0.14 0.117 0.1 1.011 XB31E11 93Y13 Prob 0.01180.0067 0.0572 0.2474 XB31E11 93Y20 Mean1 18.44 11.25 3.9 23.58 XB31E1193Y20 Mean2 18.94 9.42 3.97 21.83 XB31E11 93Y20 #Locs 9 3 3 3 XB31E1193Y20 #Reps 12 6 6 6 XB31E11 93Y20 #Years 2 1 1 1 XB31E11 93Y20 SE Diff0.112 0.044 0.044 0.52 XB31E11 93Y20 Prob 0.0022 0.0006 0.2697 0.0782XB31E11 RJS31004 Mean1 19.05 XB31E11 RJS31004 Mean2 19.51 XB31E11RJS31004 #Locs 6 XB31E11 RJS31004 #Reps 9 XB31E11 RJS31004 #Years 1XB31E11 RJS31004 SE Diff 0.121 XB31E11 RJS31004 Prob 0.013 XB31E11RJS34001 Mean1 19.05 XB31E11 RJS34001 Mean2 19.31 XB31E11 RJS34001 #Locs6 XB31E11 RJS34001 #Reps 9 XB31E11 RJS34001 #Years 1 XB31E11 RJS34001 SEDiff 0.299 XB31E11 RJS34001 Prob 0.432 R182 R183 Variety1 Variety2Statistic (%) (%) WHDFLD EMGSC XB31E11 93Y02 Mean1 54.07 7.05 7.9XB31E11 93Y02 Mean2 55.47 7.63 7.1 XB31E11 93Y02 #Locs 3 3 3 XB31E1193Y02 #Reps 5 5 7 XB31E11 93Y02 #Years 1 1 1 XB31E11 93Y02 SE Diff 0.0760.159 0.44 XB31E11 93Y02 Prob 0.003 0.0669 0.1994 XB31E11 93Y03 Mean154.07 7.05 7.9 XB31E11 93Y03 Mean2 59.68 2.27 7.4 XB31E11 93Y03 #Locs 33 3 XB31E11 93Y03 #Reps 6 6 7 XB31E11 93Y03 #Years 1 1 1 XB31E11 93Y03SE Diff 0.464 0.017 0.06 XB31E11 93Y03 Prob 0.0068 0 0.0153 XB31E1193Y11 Mean1 54.07 7.05 5.7 7.9 XB31E11 93Y11 Mean2 54.42 7.05 4.3 7.3XB31E11 93Y11 #Locs 3 3 3 4 XB31E11 93Y11 #Reps 6 6 4 13 XB31E11 93Y11#Years 1 1 1 2 XB31E11 93Y11 SE Diff 0.503 0.218 0.88 0.45 XB31E11 93Y11Prob 0.5587 1 0.2697 0.2746 XB31E11 93Y13 Mean1 54.07 7.05 5.7 7.9XB31E11 93Y13 Mean2 53.35 7.17 3.2 6.8 XB31E11 93Y13 #Locs 3 3 3 4XB31E11 93Y13 #Reps 6 6 4 13 XB31E11 93Y13 #Years 1 1 1 2 XB31E11 93Y13SE Diff 0.726 0.366 0.29 0.26 XB31E11 93Y13 Prob 0.4276 0.7798 0.01310.0228 XB31E11 93Y20 Mean1 54.07 7.05 5.7 7.9 XB31E11 93Y20 Mean2 57.237.43 5.5 7.5 XB31E11 93Y20 #Locs 3 3 3 4 XB31E11 93Y20 #Reps 6 6 4 13XB31E11 93Y20 #Years 1 1 1 2 XB31E11 93Y20 SE Diff 0.3 0.145 0.44 0.56XB31E11 93Y20 Prob 0.0089 0.1186 0.7418 0.4934 XB31E11 RJS31004 Mean17.9 XB31E11 RJS31004 Mean2 6.3 XB31E11 RJS31004 #Locs 3 XB31E11 RJS31004#Reps 7 XB31E11 RJS31004 #Years 1 XB31E11 RJS31004 SE Diff 0.2 XB31E11RJS31004 Prob 0.0151 XB31E11 RJS34001 Mean1 7.9 XB31E11 RJS34001 Mean26.3 XB31E11 RJS34001 #Locs 3 XB31E11 RJS34001 #Reps 7 XB31E11 RJS34001#Years 1 XB31E11 RJS34001 SE Diff 0.65 XB31E11 RJS34001 Prob 0.1331

TABLE 3 Soybean SSR Marker Set SAC1006 SATT129 SATT243 SATT334 SAC1611SATT130 SATT247 SATT335 SAC1634 SATT131 SATT249 SATT336 SAC1677 SATT133SATT250 SATT338 SAC1699 SATT142 SATT251 SATT339 SAC1701 SATT144 SATT255SATT343 SAC1724 SATT146 SATT256 SATT346 SAT_084 SATT147 SATT257 SATT347SAT_090 SATT150 SATT258 SATT348 SAT_104 SATT151 SATT259 SATT352 SAT_117SATT153 SATT262 SATT353 SAT_142-DB SATT155 SATT263 SATT355 SAT_189SATT156 SATT264 SATT356 SAT_222-DB SATT165 SATT265 SATT357 SAT_261SATT166 SATT266 SATT358 SAT_270 SATT168 SATT267 SATT359 SAT_271-DBSATT172 SATT270 SATT361 SAT_273-DB SATT175 SATT272 SATT364 SAT_275-DBSATT181 SATT274 SATT367 SAT_299 SATT183 SATT279 SATT369 SAT_301 SATT186SATT280 SATT373 SAT_311-DB SATT190 SATT282 SATT378 SAT_317 SATT191SATT284 SATT380 SAT_319-DB SATT193 SATT285 SATT383 SAT_330-DB SATT195SATT287 SATT385 SAT_331-DB SATT196 SATT292 SATT387 SAT_343 SATT197SATT295 SATT389 SAT_351 SATT199 SATT299 SATT390 SAT_366 SATT202 SATT300SATT391 SAT_381 SATT203 SATT307 SATT393 SATT040 SATT204 SATT314 SATT398SATT042 SATT212 SATT319 SATT399 SATT050 SATT213 SATT321 SATT406 SATT092SATT216 SATT322 SATT409 SATT102 SATT219 SATT326 SATT411 SATT108 SATT221SATT327 SATT412 SATT109 SATT225 SATT328 SATT413 SATT111 SATT227 SATT330SATT414 SATT115 SATT228 SATT331 SATT415 SATT122 SATT230 SATT332 SATT417SATT127 SATT233 SATT333 SATT418 SATT420 SATT508 SATT583 SATT701 SATT421SATT509 SATT584 SATT708-TB SATT422 SATT510 SATT586 SATT712 SATT423SATT511 SATT587 SATT234 SATT429 SATT512 SATT590 SATT240 SATT431 SATT513SATT591 SATT242 SATT432 SATT514 SATT594 SATT433 SATT515 SATT595 SATT436SATT517 SATT596 SATT440 SATT519 SATT597 SATT441 SATT522 SATT598 SATT442SATT523 SATT601 SATT444 SATT524 SATT602 SATT448 SATT526 SATT608 SATT451SATT529 SATT613 SATT452 SATT533 SATT614 SATT454 SATT534 SATT617 SATT455SATT536 SATT618 SATT457 SATT537 SATT628 SATT460 SATT540 SATT629 SATT461SATT544 SATT630 SATT464 SATT545 SATT631 SATT466 SATT546 SATT632-TBSATT467 SATT548 SATT633 SATT469 SATT549 SATT634 SATT470 SATT550 SATT636SATT471 SATT551 SATT640-TB SATT473 SATT552 SATT651 SATT475 SATT555SATT654 SATT476 SATT556 SATT655-TB SATT477 SATT557 SATT656 SATT478SATT558 SATT660 SATT479 SATT565 SATT661-TB SATT480 SATT566 SATT662SATT487 SATT567 SATT665 SATT488 SATT568 SATT666 SATT491 SATT569 SATT667SATT492 SATT570 SATT672 SATT493 SATT572 SATT675 SATT495 SATT573 SATT677SATT497 SATT576 SATT678 SATT503 SATT578 SATT680 SATT506 SATT581 SATT684SATT507 SATT582 SATT685

TABLE 4 BREEDING HISTORY FOR XB31E11 Bi-parental cross F1 growoutharvested in bulk F2 modified single seed descent F3 single plantselections made Progeny row yield test Preliminary yield testingRegional yield testing Purification - single plants selectedPurification - individual plant rows bulked together Advanced yieldtesting Bulk breeder's seed increase Elite yield testing Foundation seedproduction

1. A plant or a plant part of soybean variety XB31E11, representativeseed of said soybean variety XB31E11 having been deposited under ATCCAccession Number PTA-11648.
 2. A seed of soybean variety XB31E11,representative seed of said soybean variety XB31E11 having beendeposited under ATCC Accession Number PTA-11648.
 3. A soybean seedobtained by introducing a transgene into soybean variety XB31E11,representative seed of said soybean variety XB31E11 having beendeposited under ATCC Accession Number PTA-11648.
 4. The seed of claim 3,wherein the transgene confers a trait selected from the group consistingof male sterility, site-specific recombination, abiotic stresstolerance, altered phosphorus, altered antioxidants, altered fattyacids, altered essential amino acids, altered carbohydrates, herbicideresistance, insect resistance, and disease resistance.
 5. A soybeanplant, or a part thereof, produced by growing the seed of claim
 2. 6. Asoybean plant, or a part thereof, produced by growing the seed of claim3.
 7. A method for developing a second soybean plant comprising applyingplant breeding techniques to a first soybean plant, or parts thereof,wherein said first soybean plant is the soybean plant of claim 1, andwherein application of said techniques results in development of saidsecond soybean plant.
 8. A method for producing soybean seed comprisingcrossing two soybean plants and harvesting the resultant soybean seed,wherein at least one soybean plant is the soybean plant of claim
 1. 9.The soybean seed produced by the method of claim
 8. 10. A soybean plant,or a part thereof, produced by growing said seed of claim
 9. 11. Amethod for developing a second soybean plant in a soybean plant breedingprogram comprising applying plant breeding techniques to a first soybeanplant, or parts thereof, wherein said first soybean plant is the soybeanplant of claim 10, and wherein application of said techniques results indevelopment of said second soybean plant.
 12. A method of producing asoybean plant comprising a locus conversion, the method comprisingintroducing a locus conversion into the plant of claim 5, wherein saidlocus conversion provides a trait selected from the group consisting ofmale sterility, site-specific recombination, abiotic stress tolerance,altered phosphorus, altered antioxidants, altered fatty acids, alteredessential amino acids, altered carbohydrates, herbicide resistance,insect resistance, and disease resistance.
 13. An herbicide resistantsoybean plant produced by the method of claim
 12. 14. A diseaseresistant soybean plant produced by the method of claim
 12. 15. Aninsect resistant soybean plant produced by the method of claim
 12. 16.The soybean plant of claim 15, wherein the locus conversion comprises atransgene encoding a Bacillus thuringiensis (Bt) endotoxin.
 17. Asoybean plant, or a part thereof, expressing all the physiological andmorphological characteristics of soybean variety XB31E11, representativeseed of said soybean variety XB31E11 having been deposited under ATCCAccession Number PTA-11648.
 18. A method comprising isolating nucleicacids from a plant, a plant part, or a seed of soybean variety XB31E11,analyzing said nucleic acids to produce data, and recording the data forXB31E11, representative seed of said soybean variety XB31E11 having beendeposited under ATCC Accession Number PTA-11648.
 19. The method of claim18, wherein the data is recorded on a computer readable medium.
 20. Themethod of claim 18, further comprising using the data for crossing,selection, or advancement decisions in a breeding program.